Did any of you do a search of the forum? There is all of the information that you are looking for along with my comaprison article.
The non-turbo 944 transaxle is identicle to the AUDI 016 except thet the provision for a pilot bearing is not there and the provision for the clutch slave cylinder and fork is not there. You could use a hydraulic T/O bearing possibly and the idea about the hole in the shaft sounds like a possibility. You do not need to spend the $$$ on the 944 turbo disk. You just need to look at Ford and Chrysler discs with 1" 23 spline. They will work just fine. The early 944 has a 3.89 final drive. The turbo had a 3.375 final drive and the late non-turbo has a 3.875 final drive. Both the late 944 and turbo have a larger diameter ring gear and a larger front pinion bearing. The larger gear allowed for wider gear teeth and much increased strength. No AUDI 016 has this. The turbo-S transaxle is the strongest one because the gears and shafta are shot peened. The differential for the turbo is interchangable with the other 016 transaxles. However, you likely will not ever find a used one. They are much sought after. There is a guy that has found a late AUDI OEM Torsen that can be easily modified to fit into an 016. I should also say that the bellhousing mounting pattern is the same between the Porsche and AUDI.
The 6 spd (01E) is a good transaxle as far as I have been told. It has many of the updates from the 944 turbo transaxle including the larger ring gear and front pinion bearing. Although the ratios many say do not fit with a v8 very well. The AUDI version has some updates that the Porsche ones do not have. The biggest is first gear. The later AUDI 01E's have a wider 1st gear because of some failures (stripped teeth) on turbo cars.
The 944 non turbo 016, early or late, has a mostly useless first gear. (13.97 early and 13.95 late overall ratio)
This is all that comes to mind right now.