Mustangs Unlimited and others sell an adapter plate to use the stock clutch and linkage with a T5. The input shaft of the T5 is about 1" longer than the stock Toploader - so you need this spacer to properly mount the tranny to the existing bell housing.
The T5 trans mount is in a different position so you need a new cross member. Not sure about the drive shaft or speedo-cable. You also need to be sure of which tranny you use - the regular T5 and the World Class T5 look similar, but rear mounting position is slightly different - so be sure to get the right cross member.
I haven't done a T5 swap, but have done an AOD swap - stock drive shaft worked for me but in this case you need to use the later model yoke (requires a special u-joint to work), needed a special speedo cable to keep the VSS sensor (for EFI computer), and a special cross member for the different rear mounting position. I made a custom linkage to use the early Mustang auto shifter with the AOD. I can give details and photos to anyone interested.
I also remember Mustang Monthly doing several articles on these swaps in the past - you might try seaching there website for info.
Ron Morris Performance also offers some of the swap pieces for late model stuff going into early 'stangs.
I hope this helps.