Scapper:
I'm not 100% certain of your question so some of my answer might not make sense:
The input shaft of T5 (and many other transmissions) consists of splined shaft (which goes into clutch and gear (which mates with front gear of counter shaft). And the T5 has about a dozen different options... (length, # of splines and # of gear teeth).
The cool part: ALL Ford T5s have 10 splines of diameter 1.0625". So, with correct diameter clutch and appropriate depth bell housing you physically could put any T5 on any engine from 2.3 to 5.0.
But the internals have over 200 different options.
A '91 5.0 Mustang has 23 tooth gear/9.25" over all length input shaft. (later models <'94/95>are longer and take a corresponding longer bell housing)
The 2.3 Mustang has a 19 tooth gear/9.546" over all length input shaft.
So, you can physically put a 2.3 input shaft into a 5.0 T-5 (19t gear is smaller than 24t), but the teeth won't really engage (and the 1st time you drove it hard it would wipe the teeth off. The converse doesn't work: 23t gear of 5.0 T5 is too large.
This because 2.3l has ratios of 3.97/2.34/1.46/1.00/.79 for 1st-5th gears, while '91 5.0 has 3.35/1.99/1.33/1.00/0.68
Actually, there are 2 different 5th ratios for the 2.3l as both the counter shaft and output slide on, so you can have some interesting OD combinations.
There are at least 7 different main cases (Chev(3)/Ford(2)/Jeep/Nissan) and a dozen output housings (2wd/4wd/rotated/forward-mid-aft shifter/etc). But the gears (mostly) interchange between cases (just keep each set all together)*.
And don't blame me if they don't.
Hopefully, this helps. If not try this:
http://www.allfordmustangs.com/Detailed/349.shtml
*World class (w/c) needs to stay with W/C; non-W/C needs to stay with non-W/C.
Don