Mike,
The GT-40 combo is a great mid range small block choice. The world class t-5 may be your weak point if you like to get on it quite a bit, but I am using a super duty t-5 in my 427W stroker and don't anticipate having any problems. I say that but with my luck..... The engine set-up from ford has the front cover that can accept a mechanical fuel pump, so either route is fine. The balancer is the 50 oz. mustang style and will work with most v-belt systems. I know that the march 3-piece pulley set-up works great with this engine. The
oil pan is a rear sump model, but will work with most any Cobra replica, as there is no crossmember to get in the way. The stock bellhousing will work fine as well, and that is what I use (although I am going with a hyd. slave cylinder vice cable). The intake, carb and distributor will bolt right up, the only thing to consider is the distributor gear, as with a roller cam it must be steel not bronze. The only drawback is the water pump, as it is designed to used the mustang reverse rotation system. So that would probably be tossed. Other than that it should be a relatively easy and enjoyable engine. Let me know if there are any other questions you have, or if you need any additional technical info. I am full of useless information (and other things too).
Good Luck,
Chris