engine angle
The short of it is that if you draw 2 imaginary lines, one coming directly out the trans output and another coming out the pinion, these 2 lines must be parallel. BUT, they must not be the same line. In other words, there should be 2-4 degrees or so of offset so the cupsin the U Joints turn and get continuously lubed.
What I did for my swap was use an angle finder. I put it against the flat parts of the trans output and the diff input and made sure that those 2 angles were identical. That's for the vertical position. For the horizontal alignment, I had to make sure that the motor/trans was perfectly straight relative to the frame.
For my particular car, the driveshaft ends up being slightly angled in both the horizontal and vertical, by about 4 degrees. But the trans output and the diff input are are straight relative to each other. This means that the 2 UJoints are in phase and there should be no harmful harmonics.
The take home msg here is that the angle of the of the DS relative to the pinion or trans is not really very important (as long as it is reasonable and not some extreme angle). What IS important is the trans and the diff alignment relative to each other.
I suspect it's actually a little easier to align the Ujoints in phase with an IRS car since the diff is fixed and not moving with the suspension. In most of the old school swaps (camaro, vette, chevelle, etc.), the car had a 350 in it so the LS1 sits in almost exactly the same spot - simple. But if you were swapping into say, an MGB or something, I think it'd be tricky to position the rear axle correctly (shims betw. axle and leafs? adjustable shackles?).


