How do I line up the dowel pins in between the block and head

First place the gaskets on the head to see if they are the correct ones. Then to install, find some bolts that are the same size of the head bolts and cut off the top of them. Install then in the block, put on the head gasket , and put on the head. Then remove the bolts

1. Clean the cylinder gasket surfaces on the engine block.
2. Inspect the dowel pins (cylinder head locator) for proper installation.
3. Clean the cylinder head gasket surfaces on the cylinder head.
4. Place the NEW cylinder head gasket in position over the dowel pins (cylinder head locator).The cylinder head gasket is not directional and may be installed using either side facing the engine block.
5. Install the cylinder head to the engine block. Guide the cylinder head carefully into place over the dowel pins and the cylinder head gasket.
   
Install the cylinder head bolts.

6. Tighten the bolts in the sequence shown in the image below on the first pass to 30 [n-m] (22 lb ft).


7. Use a torque angle meter in order to tighten the cylinder head bolts in sequence on the final pass. Tighten:
   
   • Tighten the long bolts (1, 2, 5, 6, 9, 10, and 13) on the final pass in sequence to 75 degrees.
   • Tighten the medium bolts (14 and 17) on the final pass in sequence to 65 degrees.
   • Tighten the short bolts (3, 4, 7, 8, 11, 12, 15, and 16) on the final pass in sequence to 55 degrees.


8. Measure the NEW spark plugs for the proper gap.Adjust the spark plug gap if necessary.
   Specification:
   Spark plug gap to 1.52 mm (0.060 in)
9. Install the NEW spark plugs. Tighten:
   
   • Tighten the spark plugs for a USED cylinder head to 15 [n-m] (11 lb ft).
   • Tighten the spark plugs for the initial installation of a NEW cylinder head to 30 [n-m] (22 lb ft).


10. If reusing the engine coolant temperature (ECT) gauge sensor, apply sealant GM P/N 12346004 to the threads of the ECT gauge sensor.
11. Install the ECT gauge sensor.Tighten:
    Tighten the ECT gauge sensor to 20 [n-m] (15 lb ft).
    

If intake and all head bolts are removed, chances are the head is stuck to the gasket/block. The head will normally sit upon 2 dowel pins which will also,hold it secure. Use a prybar and gently apply force to the head. It will come loose

HI LIL DEB,HERE'S A LINK TO THE HEAD GASKET. Repair Guides Engine Mechanical Cylinder Head AutoZone com

The 1.6-litre twin-cam engine in your C2 VTR has a hole in each camshaft pulley, which lines up with a hole in the cylinder head. This is where camshaft locking pins should be fitted and when lined up, indicates the correct timing of the engine with piston number one at TDC. You're right, there are no timing marks, so once you've fitted the locking pins use 6mm diameter dowels or bolts if you don't have the correct tools, it's a good idea to add some paint marks to the camshaft pulleys and the crankshaft pulley. The VTR's crank can also be locked by fitting a locking pin through the engine block, just behind the oil filter. This should be done before fitting the camshaft locking pins and can be quite fiddly Citron recommend you remove the oil filter

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Left side front cylinder head



Cylinder head bolt torque sequence-3.4L engine

Cylinder head by aligning it with the dowel pins

New cylinder head bolts coated with a sealant (such as GM 1052080). Torque the bolts in the proper sequence (1-8) to 37 ft. lbs. (50 Nm). Using a torque angle meter turn the bolts 90 degrees in the proper sequence.

Left side exhaust manifold. Torque the bolts to 12 ft. lbs. (16 Nm).

Spark plugs. Torque the plugs 11 ft. lbs. (15 Nm).

Right side rear cylinder head:



Cylinder head bolt torque sequence-3.4L engine

New cylinder head gasket

Cylinder head on top of the gasket and make certain it is lined up properly with the dowel pins

New cylinder head bolts coated with a sealant (such as GM 1052080). Torque the bolts in the proper sequence (1-8) to 37 ft. lbs. (50 Nm). Using a torque angle meter turn the bolts 90 degrees in the proper sequence.

Right side exhaust manifold. Torque the bolts to 12 ft. lbs. (16 Nm).

Spark plugs. Torque the plugs 11 ft. lbs. (15 Nm).

Spark plug wires

Exhaust crossover pipe. Torque the fastener to 18 ft. lbs. (25 Nm).

Valve rocker arms and pushrods. Torque the fastener to 89 inch lbs. (10 Nm). Using a torque angle meter torque the fastener an additional 30 degrees.

Lower intake manifold. Torque the bolts to 115 inch lbs. (13 Nm).

Upper intake manifold. Torque the bolts to 18 ft. lbs. (25 Nm).

Cylinder Head Removal & Installation 3.1L Engine To Remove:
NOTE: With some minor variations, this procedure can be used on both the left and right cylinder heads.

1. Raise and safely support the vehicle.
2. Drain the engine coolant and the engine oil. Lower the vehicle.
3. Remove the upper and lower intake manifolds.
4. Remove the rocker arms and pushrods.
5. Remove the exhaust crossover pipe.
6. Remove the engine mount strut bracket.
7. If removing the left side (front) head, remove the dipstick tube.
8. Tag for identification, then remove the spark plug wires.
9. Remove the spark plugs.
10. Remove the exhaust manifold using the procedures found in this section.
11. Remove the eight cylinder head bolts, then remove the cylinder head. There are locator pins that align the head to the block. Pull upwards on the head to disengage the pins, then remove the cylinder head to a suitable work area.
12. If the head is be overhauled, remove any remaining components such as the engine lift hook, the fuel line bracket bolts, the engine coolant temperature sensor, etc., as required.

Position a new gasket, install the head, then tighten the bolts in the sequence shown (3.1L engine shown)

To Install:
NOTE: If the head gasket failed, determine the cause. Gasket failure is caused by the following conditions: improper installation; overheating due to a failure in the electric cooling fan system or a leak in the cooling system; loose or warped cylinder head; missing, off location or not fully seated locator dowel pins; low torque on the cylinder head bolts; warped block surface; scratched or gouged gasket surfaces; excessive intake manifold torque and even cracked engine block tapped holes.

1. Clean all parts well. Remove all foreign material to the bare metal. Do not use a motorized wire brush on any gasket sealing surface. It is good practice to use the proper size thread-cutting tap to clean the threaded bolt holes in the block. This helps assure an accurate torque reading.
2. Place a new head gasket on the clean engine block deck surface. Many gaskets will have some sort of marking denoting TOP or THIS SIDE UP. Make sure the gasket sits flat and is not hung up on the locator dowel pins. Use no sealer on the head gasket.
3. Carefully set the cylinder head in place, using care not to damage the gasket. Make certain that the head engages the locator dowel pins that properly position the head.
4. The bolts should be very clean since dirt built-up on the bolt threads makes it difficult to get an accurate torque reading. These are 'torque to yield' bolts which stretch a small amount when tightened; new bolts are always recommended. On a used vehicle, especially a high-mileage vehicle, it may be difficult to determine if the heads have been removed before and how many cycles the bolts have been removed and tightened. New bolts should be part of any cylinder head service. Use GM Sealer #1052080, or equivalent, on the threads of the head bolts and install all eight bolts, finger-tight.
5. With an accurate torque wrench, tighten the bolts gradually, in sequence, working from the center outwards. Final torque should be 33 ft. lbs. (45 Nm), plus an additional 90 degrees (1/4-turn). A torque angle meter is recommended.
6. Install the remaining components in the reverse order of the removal process.

Not sure what engine you have but it's the same for the 1.8L and 1.9L. Hope this helps.. Cobra!!
Installation
CAUTION: Before installing the cylinder head, check the piston squish height as outlined.

1. Clean all gasket material from the mating surfaces on the cylinder head and block. Clean out the bolt holes in the block.

1. Install the dowels. Check the dowel height (11.75/10.40). When using replacement parts, a long dowel may be encountered. A long dowel will not allow the cylinder head to sit properly and should not be used.

1. Position the cylinder head gasket on the cylinder block.

1. Apply a light coating of engine oil to the threads of the new cylinder head bolts. Install the new cylinder head bolts to the cylinder head. Following the sequence shown, tighten the attaching bolts to 40-60 Nm (29-44 lb-ft). Loosen all attaching bolts approximately two turns, then retighten the attaching bolts to 60 Nm (44 lb-ft) following the sequence shown. After tightening, turn all bolts 90 degrees, in the same sequence. Complete bolt tightening by turning them an additional 90 degrees, in the same sequence.

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Left side front cylinder head



Cylinder head bolt torque sequence—3.4L engine

Cylinder head by aligning it with the dowel pins

New cylinder head bolts coated with a sealant (such as GM 1052080). Torque the bolts in the proper sequence (1-8) to 37 ft. lbs. (50 Nm). Using a torque angle meter turn the bolts 90 degrees in the proper sequence.

Left side exhaust manifold. Torque the bolts to 12 ft. lbs. (16 Nm).

Spark plugs. Torque the plugs 11 ft. lbs. (15 Nm).

Right side rear cylinder head:



Cylinder head bolt torque sequence—3.4L engine

New cylinder head gasket

Cylinder head on top of the gasket and make certain it is lined up properly with the dowel pins

New cylinder head bolts coated with a sealant (such as GM 1052080). Torque the bolts in the proper sequence (1-8) to 37 ft. lbs. (50 Nm). Using a torque angle meter turn the bolts 90 degrees in the proper sequence.

Right side exhaust manifold. Torque the bolts to 12 ft. lbs. (16 Nm).

Spark plugs. Torque the plugs 11 ft. lbs. (15 Nm).

Spark plug wires

Exhaust crossover pipe. Torque the fastener to 18 ft. lbs. (25 Nm).

Valve rocker arms and pushrods. Torque the fastener to 89 inch lbs. (10 Nm). Using a torque angle meter torque the fastener an additional 30 degrees.

Lower intake manifold. Torque the bolts to 115 inch lbs. (13 Nm).

Upper intake manifold. Torque the bolts to 18 ft. lbs. (25 Nm).

Please clarify which dowel pins you are looking for. There are dowel pins that align the head to the block, and dowel pins that align the transmission case to the engine block. I hope this helps you.