The best of the N/A motors would be an 04 Mach 1. They had the best heads, but will be the most expensive (03 Mach 1 would be next). 99 or 01 Cobra (01 as the 99s had HP issues and not all of them were updated by Ford) would be next. After that the 96-98 Cobra. Other than the Mach 1, these will all have electronics for a manual tranny, so if you want an auto, think about the auto Mach or the Mark VIIIs (or changing the harnesses and ECM - expensive).
The cheapest and easiest to find would be 93-95 Mark VIII, but the 96-98 Marks have better intakes and COP ignition (looks much cleaner), and are ODB 2 so you can tune them without a chip (tuning a 93-95 EEC-IV ECM requires putting a chip in the diag connector and finding someone to do that might be difficult - it was going to be for me when I considered it). You can put a 96-98 Cobra intake on any of the Mark motors, but you will also need the Cobra IMRC plates for the 93-95 Mark, and maybe for the 96-98 (but I don't believe so). The Cobra intake will give you a little more at the top end, but the Mark cams limit the top end so they peak around 5200 RPM (vs. the Cobra's 6200).
Definitely get a complete donor if you can - the doodads will eat you up on these motors (my mistake). I've seen 93-95 Marks go for $500 to $1000 wrecked. The 96-98 LSC will go for a little more. If you try to buy a complete running one, I've seen some of the 98s still going for $6000-$8000, which is way too much to pay for a donor car.
If you can get the 98 Mark for a good price ($1000-$1500???), that doesn't sound too bad. You might want to freshen it up if you plan to run it hard, which is expensive - a gasket set for these motors is like $400. But I've opened up 2 Mark motors (93, 94, from which I used the block) and both had around 100K miles and the cylinders were still close enough to spec that the machine shop suggested a hone and new rings.
The Marks have some cool features like the mileage computer and compass you can use. You might even pull the power seats (I have 98 Mark seats in my Mustang - a little too big, but like a leather recliner), some good soundproofing material (pads) you can make use of, as well as the IRS (if it will fit under your car). You might even make use of the air-ride stuff if you are real creative. It probably won't let you go around corners on 3 wheels like the Low Rider guys, but you can probably drag the bumper like the mini-trucks .:dumb:
The 96-04 GTs will all have 2V motors and unless it's a Rousch or Saleen with a blower, I'd skip it. Not enough power and no eye candy.