I drove 200 miles round trip to work with 3.73's all interstate 75 to 80 with a couple throttling to merge onto the interstate... I got about 275-300 (down from 325) on a tank. I think I put in about 8 gallons a night.
Since then though I've had 2 transmission (5th gear went out both times) and shortly after the 1st transmission the rear end went out. Ford said lack of gear oil...but it never leaked so I'm not really sure what exactly happened. Now I'm back down to a 3.27 rear end out of a wrecked 2001. When I get a new one I'll probably go to a 4.10 gear set. The different between 3.27 and 3.73's is night and day on the get up and go. You top out first pretty quick. Many times in the rain I just started out in 2nd. It's easier to drive with the lower gear in it too.
Intake: Cold Air or Manifold? Cold air...nothing but sound. I've got a fenderwell CAI that I got real cheap, only problem I've had is when driving in heavy rain behind someone the mist gets into it and causes a stumble. I also have the chrome pipe (looks) going to it which absorbs a ton of heat in the summer and kills the intake air temp which causes some power loss. Intake Manifold...$1,000 (I think) for the Trickflow and you'll get I think 30 or so HP. However, for another $2,000 you can make 150+ (S/C or turbo).
Plenum: I've got an Accufab w/ 70MM throttle body. No big performance gain, but SOTP you could notice a tad. On hotter days though I get some heatsoak (could be from the CAI).
Exhaust: Also mostly sound with some improvement. Remove the cats and you lose a tad bit of torque, gain horsepower. H-pipe for throaty sound, X-pipe for the racy, raw sound like on drag cars. Get a muffler you like the sound of. The H and X-pipes will change the sound. Long tube headers only, don't waste your money on short tubes. Long tube require a different kind of midpipe from what I remember.
Gears: No real performance gain HP/TQ wise, but gives you more acceleration (read: quicker, not faster).
Cams: $600 for MPH's cams and can give you pretty decen HP/TQ numbers.
Heads: Never checked into them, but on my race car better heads = more HP/TQ. For the modular motor I'm sure it'll probably cost too much to justify on a N/A motor.
Suspension: Haven't messed with that yet. Just got an Eibach lowering kit and it helped improve cornering. I have a set of Bilstein shocks/struts waiting to go on.
Forced induction: Best bang for the buck I'd say. $3,000 and you get tons of HP/TQ. Only issues is the stock 2v motors don't have forged internals so I think MPH recommended not going above 500HP (may have been 400) with their tunes. Even then it's a ticking time bomb. With forced induction pretty much any mod you do to the engine will enhance the performance of the car more so than non-forced induction.
That about covers it.
From one of the online spee/rpm calcs.
3.27s in 4th gear at 6000RPM = 140MPH
That is accurate... Just about exact. I shifted at ~5900 into 5th and was right around 140.