Exhaust manifold on driver's side are the front and back holes; are they studs or bolts?

I suggest you use all new exhaust manifold hardware and torque new bolts to 20 Ft Lbs.
4.5L and 4.9L Engines
RIGHT
Disconnect the negative battery cable. Remove the air cleaner. Remove the exhaust crossover pipe. Disconnect the oxygen and coolant temperature sensors. Remove the catalytic converter-to-AIR pipe clip bolt. Remove the upper manifold-to-cylinder head bolts. Raise and safely support the vehicle. Disconnect the converter air pipe bracket from the stud and remove the converter-to-manifold exhaust pipe. Support the engine cradle with screw jacks and remove the rear cradle bolts. Loosen the front cradle bolts and slightly lower the Engine cradle. Remove the remaining exhaust manifold-to-cylinder head bolts, the AIR pipe, and the manifold. Clean the gasket mounting surfaces.
To install:
Install the exhaust manifold and replace the AIR pipe. Tighten the manifold mounting bolts to 16-18 ft. lbs. (21-24 Nm). Install the manifold-to-converter exhaust pipe and replace the converter air pipe bracket to the stud. Raise the Engine cradle and install the rear cradle bolts. Tighten to 75 ft. lbs. (102 Nm). Lower the vehicle. Replace the upper manifold-to-cylinder head bolts. Replace the converter air pipe to AIR pipe clip bolt. Connect the coolant temperature and oxygen sensor connectors. Replace the exhaust crossover pipe. Replace the air cleaner and connect the negative battery cable. Start the Engine and check for leaks.

It is very rare to through holes to the water jacket, especially the holes of fairly important studs and bolts. It happens mostly in die cast items such as some cylinder blocks and some holes to the oily parts are through and also some to where there is air or exhaust gas on the other side.

There is no need to despair yet even if you have drilled off course or simply gone too far. There are ways around such problems if indeed it is a problem and you won't know until you have removed the manifold and taken a close look.

There are repair epoxies and putties of various types intended to reclaim such errors and there are specialist cold stitching techniques which can reclaim almost anything made of metal. For areas that must be strong and are subjected to very high temperatures I drill and tap oversize and sometimes make a double diameter stud and sometimes I plug the oversized hole with a large bolt and machinery adhesive, cut off flush and re-drill and tap the original size.
Good luck!

Two things which come to mind are the new manifold/gasket did not seat or cracked when torqued down, or there was a problem with a stud.
For the stud, if the stud turned further into the head when the nut was tightened, it could have cracked the head. Some manifolds used bolts instead of nuts to fasten the manifold. Memory fails me which type you have, but you could check to see if all bolts have same Part# per Dealer and if different, the wrong length could have gone into the wrong place.
For Future reference, there are some new ideas in manifold fasteners by Aftermarket makers. Each fastener is 2-piece and the seats expand when the bolt is installed.
I think your new manifold cracked. Exhaust leaks sound like a knock each time that cylinder fires with the cracked port.
Would like to know what you found.

if they are the same as the manifold studs, then they are on the side of the engine, and they are what secure the manifold to the side of the engine. either that or at the bottom of the manifolds, which would hold the front portion of the exhaust pipe to the exhaust manifold. what kind of work (if any) was done that caused these to be broken?

Check this for 1996-1999 FORD 3.0L (182) V6 DOHC...
- Install the exhaust manifold with a new exhaust manifold gasket.
- Install the exhaust manifold retaining studs and tighten to 13-16 ft. lbs. (18-22 Nm) in the sequence illustrated.
Raise and safely support the vehicle.
Position the Y-pipe assembly using a new flange gasket and install all the retaining nuts and bolts loosely.
Starting at the front of the system tighten the Y-pipe to exhaust manifold nuts to 26-34 ft. lbs. (34-46 Nm).

- Tighten the converter to transaxle nut and bolt to 30 ft. lbs. (40.3 Nm). Tighten the converter outlet bolts to 26-34 ft. lbs. (34-46 Nm).



Fig. Right side exhaust manifold mounting bolt tightening sequence-3.0L DOHC engine (click image for zoom)




Fig. Left side exhaust manifold mounting bolt tightening sequence-3.0L DOHC engine (click over image for zoom)

Hope this helps (remember to rating this answer).

the fronts are studs and all the rest are bolts

Removal & Installation

2.2L Engine

1. Before servicing the vehicle, refer to the precautions section.
2. Disconnect the negative battery cable.
3. Drain the engine coolant.
4. Remove or disconnect the following:
   Exhaust manifold, if equipped with n automatic transaxle Right front wheel Splash shield Water pump sprocket access plate from the timing cover
   
   
   
   Fig. Remove the water pump sprocket access plate from the timing cover -2.2L engine
   
5. Attach Water Pump Sprocket Holding Tool J 43651to the sprocket using the access plate bolts to secure the tool to the engine front cover.
   Sprocket to water pump bolts Engine block to water pump bolt Engine front cover to water pump bolt Thermostat housing to water pump feed pipe 2 water pump to engine block bolts Water pump
   
   
   
   Fig. Water pump mounting-2.2L engine
   

To install:

1. Use a threaded stud in the water pump hub to align the hub to the water pump sprocket.
   Water pump and bolts Thermostat housing to water pump feed pipe Engine front cover bolt and engine block to water pump bolt. Tighten the bolts to 15 ft. lbs. (20 Nm) 2 of the water pump sprocket to water pump bolts
   
2. Remove the threaded stud.
   Last water pump sprocket to water pump bolt and tighten the sprocket bolts to 89 inch lbs. (10 Nm).
3. Remove the tool.
   Water pump sprocket access plate to the timing cover and tighten the bolts to 89 inch lbs. (10 Nm) Splash shield Right front wheel Exhaust manifold, if removed
4. Fill the cooling system.
5. Connect the negative battery cable.

2.4L Engine

1. Before servicing the vehicle, refer to the precautions section.
2. Disconnect the negative battery cable.
3. Drain the cooling system.
4. Remove or disconnect the following:
   WARNING Do not rotate the flex coupling more than 4 degrees or damage may occur. Oxygen Sensor (O 2 S) electrical connector Exhaust manifold heat shield Coolant inlet housing bolt through the exhaust manifold Exhaust manifold brace-to-manifold bolt Manifold-to-exhaust pipe studs Coolant inlet housing-to-water pump cover bolt Exhaust pipe from the exhaust manifold by pulling it downward Coolant inlet pipe from the oil pan Brake vacuum pipe from the camshaft housing Exhaust manifold from the cylinder head Heater hose from the heater outlet pipe Timing chain cover and tensioner Water pump cover-to-engine bolts 3 water pump-to-timing chain housing nuts Water pump and cover assembly Water pump cover from the pump
   
   
   
   Fig. Exploded view of the water pump mounting-2.4L engine
   

continue...

96 escort 1.9L




Engine Components
Item Part Number Description 1 6766 Oil Filler Cap 2 6A548 (8 Req'd) Valve Cover Bolt 3 6582 Valve Cover 4 — Exhaust Manifold Shield-to-Exhaust Manifold Nut (4 Req'd) 5 9A462 Exhaust Manifold Shield 6 — Exhaust Manifold Shield Stud (4 Req'd) 7 9430 Exhaust Manifold 8 9454 Exhaust Manifold Nut 9 9448 Exhaust Manifold Gasket 10 — Exhaust Manifold Stud (Fine Thread), Short (4 Req'd) 11 — Exhaust Manifold Stud, Long (1 Req'd) 12 — Exhaust Manifold Stud (Medium Thread), Short (1 Req'd) 13 6518 Valve Spring Retainer Key 14 6514 Valve Spring Retainer 15 6513 Valve Spring and Damper, Intake 16 6C515 Valve Tappet Guide Plate Retainer 17 6571 Valve Stem Seal 18 6513 Valve Spring, Exhaust 19 12405 Spark Plug 20 6269 Camshaft Thrust Plate 21 — Camshaft Thrust Plate Bolt (2 Req'd) 22 — Cup Plug 23 6B273 Camshaft Oil Flow Control Rod 24 6K292 Camshaft Front Seal 25 6256 Camshaft Sprocket 26 6278 Camshaft Sprocket Washer 27 6K252 Camshaft Sprocket Retaining Bolt 28 6L269 Camshaft Sprocket Key (5 x 18) 29 6250 Camshaft 30 6051 Head Gasket 31 6A008 Cylinder Head to Block Dowel 32 6010 Cylinder Block 33 6507 Intake Valve 34 6505 Exhaust Valve 35 6049 Cylinder Head 36 — Intake Manifold Stud (7 Req'd) 37 17A084 Engine Lifting Eye 38 — Engine Lifting Eye Bolt (2 Req'd) 39 9439 Intake Manifold Gasket 40 — Bolt 41 9723 Accelerator Cable Bracket 42 9424 Intake Manifold 43 — Intake Manifold Nut (7 Req'd) 44 9D476 EGR Valve Gasket 45 — Exhaust Gas Recirculation (EGR) Valve Bolt (2 Req'd) 46 9D475 EGR Valve 47 — Fuel Injection Supply Manifold Bolt
(2 Req'd) 48 9F593 Fuel Injector 49 9D930 Fuel Charging Wiring 50 6786 Oil Level Indicator Tube Bracket 51 — Oil Level Indicator Tube Bracket Bolt 52 6754 Oil Level Indicator Tube 53 6750 Oil Level Dipstick 54 9D280 Fuel Injection Supply Manifold 55 — Vacuum Fitting 56 9E498 Main Emission Vacuum Control Connector 57 — Vacuum Tap 58 — Vacuum Hose 59 9B989 Throttle Position Sensor 60 — Screw and Washer 61 9F782 Throttle Position Sensor Gasket 62 — Throttle Body Bolt (4 Req'd) 63 — Idle Air Control (IAC) Valve Bolt
(2 Req'd) 64 9F715 Idle Air Control Valve 65 9F670 Idle Air Control Gasket 66 9E926 Throttle Body 67 9E936 Throttle Body Gasket 68 — Vacuum Fitting 69 — Camshaft Position Sensor Screw 70 6B288 Camshaft Position Sensor 71 8255 Water Hose Connection Gasket 72 — Water Hose Connection Bolt (3 Req'd) 73 8592 Water Hose Connection 74 8575 Water Thermostat 75 6065 Cylinder Head Bolts 76 6500 Valve Tappet 77 6K512 Valve Tappet Guide Plate 78 6564 Rocker Arm 79 6A528 Rocker Arm Seat 80 6A527 Rocker Arm Bolt (8 Req'd) 81 — Ignition Coil Mounting Bracket Bolt
(3 Req'd) 82 18827 Noise Filter Condenser 83 — Ignition Coil Mounting Bolt (4 Req'd) 84 12259 Spark Plug Wire Set 85 12029 Ignition Coil 86 12043 Ignition Coil Mounting Bracket A — Tighten to 5-12 Nm (4-9 Lb-Ft) B — Tighten to 5-7 Nm (3-5 Lb-Ft) C — Tighten to 21-26 Nm (16-19 Lb-Ft) D — Tighten to 2-10 Nm (1.5-7 Lb-Ft) E — Tighten to 8-13 Nm (6-9 Lb-Ft) F — Tighten to 40-55 Nm (30-41 Lb-Ft) G — Tighten to 16-20 Nm (12-15 Lb-Ft) H — Tighten to 20-30 Nm (15-22 Lb-Ft) I — Tighten to 8-10 Nm (6-8 Lb-Ft) J — Tighten to 8-11 Nm (6-9 Lb-Ft) K — Tighten to 23-30 Nm (17-22 Lb-Ft) L — Tighten to 20-40 Nm (15-30 Lb-Ft) M — Tighten to 4.5-7 Nm (3-5 Lb-Ft) N — Tighten to 18-26 Nm (13-19 Lb-Ft)

You will be very lucky to extract the studs whilst in the vehicle. Drop the front pipe. Sounds harder, but, in reality, much easier.