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I just bought 2 xs400's that had been in storage for 10 years. Im building one bike with the two. The one engine only had 8000 miles on it and the other bikes frame was in better condition. So I did an engine swap. I used a manual and did all the right steps when installing the other engine. I got it all reconnected and cleaned up. I filled it with 2 quarts of oil and put new gas in it. Went to start it up and after about 15 seconds of cranking it a loud bang was emmitted from the exaust pipe. I thought it might be a carb setting so I adjusted the carb. I tried to start it up again and every once in a while it would pop quietly, but it still wouldn't start. I don't have any idea why it wont start. Does any body know why it wont start?

Not near enough info yet... but your off to a good start as you mentioned a manual!

My 82 xs400 needed 3.3 qts of oil, might want to double check that. Have you done a compression test? Did you clean the carbs? Did you replace spark plugs?

I cleaned the carbs and im sure gas is going to both. i checked that by opening the drain bolts when the tank was set to primer. I used the sparkplugs off of another bike that had been running. Im going to get more oil to add tonight, maybe that wil help. The loud bang isnt happening anymore but still minor backfiring every once in a while. If theres backfiring wouldnt that mean there is spark?

backfire means you should be getting spark. The fact that it's igniting in the mufflers probably means there is little or no compression. If you don't have a compression tester, take out one of the plugs and cover the hole with your thumb while cranking the engine over a few times. No matter how hard you push your thumb, the compression pressure should blow it off the hole.

Any tips on how to get more compression? Tonight I filled it up with oil. Checked for spark and both plugs are firing. Still backfires.
It did something new: When I cranked it for a while it would just stop trying to start, I tried to turn it off then back on and it still wouldnt try to start. After letting it sit for a minute I heard it click and then it would try to start again. Whats that mean?
Where do I go from here?

Fuel at the drain bolts only means your getting fuel to the floatbowls, the jets could still be clogged and stopping fuel from getting into the cylinders, a much more likely scenario actually.

But your backfire sorta points to some fuel getting by, as well as spark. What did you adjust, and what way did you adjust it? Richer or leaner? Your probably on the right track looking at the carbs, but you may want to check that you didn't connect the coils in the wrong order or cross a plug lead or something, not that it should matter if it's a 360* twin with a wasted spark like I'm guessing it is. But have a good look at the ignition wiring just to be sure.

I adjusted the throttle bolt. Ive been trying it diffeerent ways to see if it would act different but it wont. When I originally cleaned the carbs one of the floats seemed a little stuck. Could a stuck float do something like this? If someone has a good way to "reset" a carb to the way it was orginially setup (if possible)?

A click wen you're trying to start means your battery is dead and needs to be charged......

Are you using the choke when starting?
How well did you clean the carbs? they need a thorough cleaning or 2, or 3 after sitting that long....

Get hold of a compression tester and check to be sure....
clean and properly gap the plugs

Have you checked valve clearance?

I put new sparkplugs in it and recleaned the carbs. Now when i try to start it smoke comes out of one pipe and it wont start. Ive checked compression and its good. Ive got spark from both plugs. Where do i go from here?