Not such a huge problem. you can still do it but you need to change some parts. I am assuming you have the T5 adapter plate for the 6-bolt bellhousing correct ?
You have 2 choices but either way you will still need to get a 5 bolt bellhousing and separator plate. Look on ebay, the 5-bolts are on there from time to time. Usually they cant give them away. You can also try David kee's toploaders. he has bellhousing and may have a 5 bolt. you will just have to pay a premium for it.
Once you have a 5-bolt bellhousing, Your choices are;
A. Take your 6 bolt adapter plate and your 5 bolt bell housing to a machine shop anf have them line up the the center hole and transfer the 4-hole locations from the bell housing to your plate. then bolt your plate to your bellhousing. They will charge you $50 - $75 to do this.
B. Buy the T-5 Adapter plate for the 5 bolt bellhosuing. CJ Poney parts sell them for the 5-bolt bellhousing. P/N T5AP1. they are about $135. A little pricey so thats why i suggest option A.
You do have the correct cross member for doing a T-5 swap in your
stang correct ? The standard cross member wont work, besides, you need the one that allows your Emergency brake cable set up to be re-attached. CJ Poney sells those to.