All manufacturers have their low-points....i.e. GM has their short/long water pumps, having to run buttons/special timing covers with roller cams, etc., etc. It's just something you have to muddle through.
As for your transmission/bellhousing, I would recommend figuring out what transmission that you'll eventually switch over to. The T5 transmission most likely won't last long behind an FE with any kind of power. There are exceptions to every rule, but I wouldn't hold my breath. Until then, there are bellhousings available from Quicktime and some other manufacturers that will allow you to use a T5 transmission and then upgrade later to a TKO 500/600.
The T5 has the same diameter input shaft as a small Toploader transmission (1-1/16x10), but it is longer. It is not the same as a TKO 600 (1-1/8x26). So if you plan to do some switching later on, you may have to do some clutch disc switching as well. The mounting pattern is also the same as a Toploader, along with the TKO's.
I think you can get adapter plates to adapt a T5 to a Toploader bellhousing, but I never did like the adapter plate idea. It seems like a cheap fix to me, that introduces more manufacturing tolerances.
If I were going to go with a temporary T5, I would aim for a World Class T5 out of the Fox Mustang line.
I sell everything that you'd need for the swap. Feel free to email me with more questions or for some pricing.
brent@b2motorsportsllc.com