1994 BMW 325 drive shaft

There is enough room to get the flex disc in there, push the driveshaft back, it is on a spline shaft and will push back far enough to get the disc in there.

The trans is in the drive shaft is out. The flex disc is out. There is a yoke with 3 bolt slots on the shaft of the trans. The haynes manual shows the bolt heads alternating position. I cannot feed the bolts for the flexplate through the bolts lack clearance. All six can be fed through the flex disc with all 6 nuts facing the transmission, Will this really matter or will removing the trans shaft nut also remove the yoke. See original submission.

I get what you are saying now. The bolts can go in from the back, it will be fine. Also notice the disc is directional.

My second problem is I may have forgotten the orientation of the flex disc. Can you give me some advice on the proper orientation? And will removing the rear trans nut also remove the yoke that the flex disc is mounted to. I have the tools but am a bit reluctant to loosen it up then reloctite the nut if it doesnt remove the flange that the flex disc bolts into.

There is no need to take the flange off. The disc has darts or arrows on it. These are to be lined up with the flange, in other words, put the bolt in the hole and in the direction of the darts and then into the flange.