The good news is if you've got the right mount kit from Ron, you will hopefully be at 3 degrees. The T5 cross member will drop the rear about a degree, the lower engine mounts should take back that degree. So with a bit of luck you should be right back at stock, with a slightly lower center of gravity (very cool!). I'm using a modified set of '65 mounts for that same reason (but with a bit less NVH).
So step one would be to install the engine and transmission, and use an angle finder to compare the angle of the drivetrain with the angle of the rockers (which are suposed to be parallel with the longitudinal centerline of the chassis). The differnce between the angle of the rockers and the angle of the drivetrain should be as close to 3* as possible, but no greater than 4* (this is from my personal experience. Above 4 degrees and I have trouble getting the pulsing vibrations stopped). End of step one.
Step two. pull the old rear end and set blocks under the axle mounting pad of the springs so the vehicle sits on those springs with the new axle sitting on the new spring perches on top of the springs, and centered side to side. I lightly tighten the U-bolts so that I can turn the housing inside, but it won't slip by itself.
Get a whole bunch of real cute looking girls to sit on the car, until you get it to to match the final curb weight with driver and about 1/2 tank of gas(at each corner if you can, but at minimum front and back) . Cute girls are much better than beer guzzling budies fat butts denting things. Or you can throw lots of weight in the trunk (maybe two fat buddies and a 6 pack... make sure to close the trunk lid!). with the car weighted correctly on the suspension, measure the angle of the engine-transmission, and set your pinion angle to match. Tack weld the perches, then pull it out and weld as per the above guys said. Small welds alternating side to side, allowing time to cool between welds, until you have both sides done.
Don't forget to make sure the rear end is still centered after the tack weld. For that you need to ensure you have good stiff bushings and straight springs, then you can measure from the spring to the axle flange. I don't like using the fender lips to measure, as I've seen quarter panels welded way off, and then the rear end is off set in comparison to the chassis. It may "look" right, but it won't drive right.
When you're all washed up and back from dinner you can let your buddies out of the trunk and run like hell!
That's really about all there is. I use this oportunity to check for chassis twist by measuring both rockers and comparing the angle, and I also check to make sure the rear end is perpendicular to the longitudinal line of the chassis. Then I check the distance from the center of the axle to the center of the spindle on each side and compare lengths. They should be very close to the same The only difference should be if the caster on one side is set different than the other side.
These last steps help ensure I have a good straight chassis for a great drving car.
Hope this helps,