Bolt are good - Cars & Trucks

If you can insert a pry-bar, such as a large flat screwdriver between the tensioner and the engine it may help. Pull or push on the handle of the screwdriver while you slowly turn the bolt.
It might take a bit of pressure, but this sometimes allows the bolt to get a purchase on good threads allowing you to remove it.

If you remove the water pump and the shank if the broken bolts are exposed,try removing them with a bolt extractor.you may have to heat it up with a small torch. A propane torch used to sweat plumbing fittings will work.If the bolts are broken off in the block you will have to center punch them and drill them out.

drill a hole in broken bolt get a easy out , good to have a spray can of MOVE IT !!!! really good stuff!!! spray on the move it put easy out in the hole , heat up broken bolt when Move it starts to bubble try backing it out !!

Thats not going to be easy then. Have you tried heating the bolts or caliper brackets were the bolts are threaded. You will have to have a good torch for this one. Spraying the bolt thread area might help disolving the rust, but no likly.
good luck.

cylinder head bolts 52-55 ft lbs. engine cold 59-63 ft lbs. engine hot

rocker arm shaft bolts 15-20 ft lbs.

intake manifold bolts 11-15 ft lbs.

exhaust manifold bolts 22-30 ft lbs.

valve cover bolts 79-81 in lbs.

A good way and the right way is to use a tap to clean the thread and then the bolts will go in good, if this has been sitting for years then its a good idea to retap them, use a bolt to get the correct tap. good luck.

start with torque, 168in-lbs all bolts. Step 2.............29ft. lbs. Step3...............36ft. lbs.These first 3 steps are for all bolts at same time. each step do all bolts. Now the next steps do 1 bolt at as time until finished Then move to next. Step4............... loosen 3 turns, Step 5.................long bolts(inside row) 30 to 36ft. lbs. ..............................short bolts(outside row) 15 to 22ft. lbs. Step 6.................tighten 180 degrees then move to next bolt in sequence Sequence.......#1 Insiderow 3rd bolt back, #2 outside row 3rd bolt back, #3 insiderow 2nd bolt back, #4outsiderow 2nd bolt back, #5 Insiderow last bolt at back, #6 outsiderow last bolt at back, #7 insiderow first bolt, #8 outside first bolt. I hope that helps you get your engine together without any problems. Good luck you should be in good shape now.

Couple of things you can try, blast that bolt with PB blaster, let sit for a few minutes, and take a impact wrench to it. that doesnt work, try a torch and heat the bolt up and then crank on it. or take some ice to it and crank again, one of those will work. Pneumatic tools work best.

Good work discovering the missing bolts. You didn't say if it's a manual or auto tranny,Check out the below site for a great diagram of the mounts and bolts, and the prices are good for OEM parts. Let me know if this doesn't help.
www.hondapartscheap.com/southbay/jsp/prddisplay.jsp?hidSwitch=&hidIrno=&catcgry1=CIVIC&catcgry2=1998&catcgry3=4DR+LX&catcgry4=KA5MT&catcgry5=MT++++++ENGINE+MOUNTS&vinsrch=no&ListAll=&prdrefno=&act=&count=0&quantity=0

if you can access the bolt with a dremel tool, you can grind new flats in the sides and try a slightly smaller six pointed socket. If you have an arc welder, you can weld another good bolt to the top of the rounded off bolt head and use the head of the good bolt to undo it.