I can't tell you what your own personal preferences are, but here are some of mine:
Behind any built motor, I'd want to see an aftermarket transmission, as the T5 is like a toothpick and actually rated, for some years, lower than the torque that the 5.0 put out. A TKO of any kind or a T56 should do the trick.
I'd personally be looking for a fuel injected motor, not a carbed motor, but that's certainly personal preference. A premium set of heads is a must for me. I'd want to see a set of AFRs or Trick Flows on the car, because you can't go wrong with those brands, but there are other nice brands like Edelbrock, FMS, that can make plenty of power and are reliable proven combos. The size of the heads should be big enough to support the engine. For example, an AFR165 head on a 302 is an excellent part. However, an AFR165 on a 347 is a mismatched part, because it's going to give up a lot of power on the top-end to a AFR185, or a ported Twisted Wedge head. Premium heads are big money items, and pretty much requires complete removal of the top end of the motor and accessories to replace. The intake and cam are less expensive, but should match whichever heads you have. Post the combos up here and we'll give you 20 different opinions, but the consensus will certainly let you know if you're headed in the right direction.
As a general rule of thumb, a standard 331 has no inherent advantage over a 347 until you reach big-boost big-power aftermarket block engines. If you're looking for a stroker, the slight preference should be to the 347, but if that can easily be outweighed if you find the right combo/car in the form of a 331. Realistically, a 331's only giving up 20-25 hp at best over an identical 347, but a 347 with a mismatched or poor combo will be a turd compared to a 331 with the right parts.
Other expensive parts: forced induction kits, premium suspensions (MM and Griggs can cost 10 G's or more for a complete build), aftermarket blocks w/ internals, complete disk brake systems, built rear ends, and I'm not just talking gears w/ axles which are both easy and only a few hundred to do.
That's all I've got for now. gotta get to sleep.