Last week I pulled the timing chain cover to replace the chain, and I found that when the dots on the crank and cam gears are aligned at TDC, the distributor is at cylinder 6. I rotated the distributor back around to 1 and put everything together(with the timing dot marks lining up on the proper diagnol), and now it won't start. I'm certain the crank and cam are misaligned, but I'm unsure of the easiest way to realign everything. Any suggestions? This has been puzzling me because if the dots line up, everything should be in order, right? Also, if I pull the distributor out and rotate it 180 degrees, it will start.

Yes, the timing marks on the timing set line up the cam for firing on #6. Firing of #1 is 180° of cam and distributor rotation which is why the engine will run there. So if you ever have to do this job again simply rotate the crankshaft 360° and set the distributor on #1 or leave it and set the distributor to fire #6.

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Joshua