The auto tranny and teh manual tranny have the same issues. Beleive it or not....only the clymer manual describes both the tools and gauges....simple....needed to align the tranny correctly. This is crucial to keep from putting tenion on the tranny case. It misaligns the oil pump drive and input shaft....read that as puts a bend in it while it runs....wearing things out. The four speed has teh same issue.
This is actually simple. Just remember...that the tranny in the type 4 absorbs "0" load. Thats right....none! The tail bushing is the same part numer wether auto or manual. It also does the same thing. It is simple a bumper to arrest movement of the drivetrain package. On the 411/412....100% of the engine and tranny load....yes 100%....is held by the cross bar that is over the area where the engine bols to the tranny. The rear hanger bar bushings are simply there as bumpers as well. The entire package pivots slightly about the center hanger bar.
The object is this. You want the rear hanger bar bushings with the long bolts on them...to not have more than about 1/8th to 3/'16" crush on them.....AND simultaneously....the metal tube in the center of the tranny tail cone bushing should be almost exactly centered in the middle of the tube in the suspension. This is so that the bushing surrounding it....has not more than about 1/16" crush touching the tube anywhere. The three feeler gauges are described i the clymer manual....and are easily made with 3 pieces of flat 1/2 wide cheap steel from home depot...a dremel tool and a caliper.
How to get this adjustment? The first primary adjustment is made in the general height of the package. You will notice that there is a center hanger bar with the two funcky "EYE" bushings on it where it bolts to teh tranny. Above it....where the rubber bushings bolt to that bar...are two 13mm bolts each side. Underneath each one of those rubber bushings where it contacts the bar....is a stack of shims. They are slotted...so all you need do is losen the two bolts on each side and you can slip them in or out. By the way....these shims are identical to the control arm shims of a Saab 900....late 70's to about 88...

...identical in every way. There are about 8 of them on any given Saab...so they are easy to get.
You have about 8 on your 411/412.
The actual slewing of the package from side to side.....is done at the rear hanger bar. Look up next to the ends of the hanger bar. There are three adjustments at each end. The two horizontal 13mm bolts that go through each end of the hanger bar...are in slotted holes. When you are done getting the tail cone bushing correct...thos bolts should be in the top end of the slots. If not...then the shims are wrong on the middle hanger bar.
The vertical ut on the stud at each end of the hanger bar is to tip the end of the tranny bushing upward or downward....but once you do that...again...pay attention to the two horizontal locking bolts to make sure they are very close to the top of the slotted holes.
The third adjustment is the actual mounts for thr end of the rear hanger bar. There are two 13mm bolts. The whole mount can slide backward and forward and from side to side...to slew the whole drive train package. This is the course adjustment. Do this first.
One thing to look at...is that there is about 1/8" left beween the plate that bolts to the back of the tranny with the bushing on it...and the rear suspension crossmember. Also...looking from below at the parralellism between the bushing plate on the back of the tranny and the cross member will tell you wether the the whole package is align axially to the centerline of the car. If the bushing plate is not exactly parralel to the crossmember that holes the trailing arms....then loosen the rear hanger mounts at the end where the are bolted to the body...and tap the whole package one way or the other. Ray