I recently had my 96 Honda civic lx Manual trans start having a cylinder 3 misfire. I replaced spark plugs and wires. And did a compression test to find out that cylinder 3 has very low compression around 50. When I rev it it seems to go back up around 150-180. Where do I start on how to fix?

 

Find out why it has a low compression? blown head gasket? bent valves? ring land? Either way, you'll need to pull the head off and visually inspect them just to be sure. It's not bad pulling the head off. D-series are easy to work on.

If it's the rings, drop your oil pan, drop your crankshaft and pull the piston in cylinder 3 out and inspect. If you go this far, might want to replace all the rings on the other cylinders and check your piston bearings and crank bearings for any scratch marks that your finger can feel it. Replace those if your finger caught any scratches. If you are replacing the rings, make sure you hone your cylinders and clean it well with brake cleaner before dropping your pistons with new rings back in.

Don't need to spend a lot of money, just ebay the whole replacement parts like I did. Still runs amazing with cheap ebay parts 77k miles so far with the rebuild. The only thing I spent a bit more was Felpro head gasket that I bought cheap on ebay as well. The rest are cheapest ebay parts I could find.

 

The shade-tree "leak-down" test will tell you generally where the air is getting out which is kind of all you need here.

spark plugs out, valve cover off, loosen and lift the rocker assembly enough that the valves can all seat (don't waste the time removing fully yet).

apply low pressure air to the cylinders through the spark plug hole/tube. If your compression tester comes with the fittings, use that. I use a blow gun with a large rubber tip that seals to the plug tube. this doesn't need to be fancy, it just needs to seal up. regulate the air down on your compressor to minimize the chance of rotating the crank. 20psi is plenty.

you're listening for the air flow from the exhaust, intake or crankcase (tailpipe, throttle body, oil fil cap) you may hear it all three places... but my guess is the exhaust valves have burnt. I have seen it several times on these engines. Carbon builds up on the exhaust valve seat creating a small, unnoticed leak. then the blow by erodes the edge of the valve until it starts to misfire. If you find one like this, make sure the rest are cleaned and re-lapped like Silentz mentioned so you won't need to have it apart again any time soon.