Well at idle my engine is shaking from side to side. The balancer doesn't move at all (checked that one first). I'm thinking maybe my engine mounts are just worn out since I stupidly didn't replace them during the engine swap. Then engine is running better than ever right now, and I can't hear any problems in the engine or from the exhaust so I don't think I am missing in a cylinder. I also have a cam in it, and I suppose at low enough idle it might do that, but I didn't think my powermax 2030 was extreme enough to do that.

Also, my alternator is making funny noises???

 

This sounds like what my car was going through last month. I heard a noise from the alternator and my engine shook the car at idle and accelerating in overdrive. One of my spark plug wires burned through so I changed the plugs and wires, which fixed the shaking. Then I replaced the alternator but that didn't get rid of the sound, so I guessed it was the automatic belt tensioner and replaced it, no more sound.