Is the engine running or are you rebuilding it? That'll direct a lot of the advice your likely to get. I assume by "put together" you mean its pulled and apart on your garage floor. If this is the case what are your goals?
If I were you I'd consider stroking it. The extent to which you stroke it will likely be debated, personally I don't have experience but some people prefer the 331 as they claim its more durable than the 347. Due to the piston rod length on the 347, it tends to create more of a side load on the cylinder wall of a stock 5.0 block (aftermarket blocks don't have this problem as they tend to beef up the problem areas of stock blocks). This causes excessive wear which will eventually cause blow by and you'll lose compression. As I said I have no personal experience but read a decent amount about it so maybe someone else can chime in.
Assuming you went the stroker route your definitely going to need to upgrade your stock intake, exhaust headers, cam, heads, and computer.
Headers are easy, go with long tube, preferably ceramic coated if you have the cash as this will keep down temps under the hood.
AFR and Twisted Wedge seem to have just about the best reputation I can find. The pros of AFR is that if you don't go crazy with the intake/exhaust valves you can keep your stock pistons (if your not stroking it) and you should get a fairly notable increase in power. Twisted Wedge require notched pistons, so if your considering stroking it consider pistons designed for this head. I have read that for a 302 (5.0) you should keep the intake/exhaust around 1.90" and 1.600" respectively to keep velocity up, this again changes if you are to stroke the engine as you'll want larger valves as to not choke the flow. Plus being aluminum heads you save ~50 lbs total so given your mustangs lbs/hp ratio thats another couple hp.
As far as the intake and cam I can't really help you. I have little experience messing with MAF but I hear its mod friendly.
Not sure if thats what your looking for but I thought I'd thorough some stuff your way since you were a little vague on what you were looking for.
1966 Mustang presently in restoration