engine and transmission problems after pi swap

yea, your right, ok lets see...

A little while ago I installed a pair of PI heads, intake and cams everything went well untill start up. First started up and it vibrated like crazy, we found that the harmonic balancer was damaged in the installation process (my fault)... I bought a new one and installed it, vibration went down a little, but the engine seems to be uneven. As in at low rpms the engine runs rough, in mid rpms its almost unnoticeable(vibration) and in the upper range it finally pulls harder then the npi i remember.

OK, so during this time the transmission starts to knock (ugghh).It only knocks when the clutch is engaged I blame the vibration from the engine f**king with the bearings in the trany. Plus I started noticing problems with the trany after i tried power shifting one time...(promise just that once).

Since this I've done several tests for both problems and a few videos of different noses its making.

YouTube - knock in trans

YouTube - engine shake and uneven start....

engine tests done:
That was tests on the fuel:
First test was done before i installed the intake/heads, it was the injectors on my npi set up. I just threw them in there to see if they worked (got them used). They worked fine after the tune learned them. Even gas mileage was not bad. I tested also by unpluging one at a time while running and listening for a difference in idle (if no change then that one is a problem cylinder) and they all changed in the same manor...

Tests done on the ignition:
First i tested the wires, (5000ohm/foot) and they were fine, i first gapped the sparks to .04 during the swap becuase i heard it would run better with high compression, i decided to change it back becuase of the problems i'm having now. I tested the primary and secondary ohm reads on both coils and the secondary was a little higher then the haynes manual said, it was at 13.25k ohms when the manaul said that it should be between 8.7k and 11.5k ohm... primary was ok with .6 to 1.0 ohm and it was at .9ohms.

Tests done on the compression:
Compression tested it, tested nicely with 200psi everywhere besides one cylinder at 185psi. I hear that 10%difference is fine for street so i assume my 7.5% is fine...

Tests that will be done on intake manifold:
I'm designing a pvc apparatus that i will put a air compressor nipple at the end. It will have a regulator so i can adjust the pressure to a reasonable psi level. I am going to put about 20-30 psi threw the throttle body(with stopped engine of course) and see if there are any leaks and where. Its basically a leak down test for the intake manifold.


tests done for transmission:
First i disconnected the cable from the clutch arm and pulled it all the way back so the TOB is off the pressure plate. It still made that noise...

Second I put the rear wheels in the air and started it and put it in first and let the wheels spin in the air. I listened for trany noises with a screw driver and the sounds seem to be coming from the rear of the trany.

Then lastly i turned the car off and had a friend turn the wheels with his hands as i held the clutch down in a few gears. It was very noisy all the gears... He then rocked it back and forward (wheels) at all the gears had play besides 5th really and noisy, really noisy




OK, soooo
this is what I've been thinking.
possible reasons:

one of the cams off by one tooth?
^ how can i tell if its off by one tooth, anyone experience this. How can i check to make sure. Like at TDC where should the notch in the cams be on both sides?

leak in intake
^my ghetto intake leak down test should tell me so


what else could it be????? arghhhh this car will be the death of me....

found the engine problem, and the transmission problem was becuase of the engine shaking becuase that stopped as well.
I had the passenger cam off by 180 degrees, i feel stupid now. but its back together and running like a champ! she pulls very well in the upper rpms now.