A T5 will not bolt up to a '54 car bellhousing. If yours does, then it sounds like the bellhousing has been changed. The input collar diameter is also larger on the T5 than on a'54 or earlier bellhousing.
If I were to guess, It sounds like you have a later bellhousing that has been modified to accept the downward angled clutch fork (which is unique to the 49-54 cars) which also means that it may not have been modified correctly to do this. I posted a picture awhile back showing the differences between the 49-54 and later bellhousings. I can't remember which post it was under though...
