Your best bang-for-the-buck upgrade will always be heads. No question.
Most performance cams don't add torque - they just move it from the lower end to a higher RPM range, usually through tricks like increasing overlap. While that makes better power up top, it can make your car\a lot slower if you just 'step on the gas' while at modest RPMs. At low RPMs, too much overlap means part of your intake charge is getting sucked out the tailpipe as the previous exhaust leaves. That leads to poor power, and lousy economy. On the top end, that actually helps fill the chamber though, which brings power back up and makes good horsepower. Fine for drag racing, so long as you can keep your engine in its 'happy place'.
If you increase the breathing capacity of your heads within reason, your engine isn't limited by the size of the ports, and can breathe freely, making more power even with a modest cam that doesn't have a ton of overlap.
ANY aftermarket aluminum head, Edelbrock included, will make a lot more power than any stock head including the GT40Ps. If you want the best for street use, for a small block street-driven Windsor, that would be the AFR 165 Renegades. If you want cheap, Skip White's NKB heads would be a great choice. Edelbrock is somewhere in the middle. Try to keep your runner volume below 170CC, as having a giant sewer-pipe intake runner means your little Windsor won't be able to keep velocity up and stuff air into the cylinder effectively with pulse harmonics. Trick Flow heads are definitely the equal of AFR heads when it comes to peak power, but for street use, the AFR design is a shade better due to port and chamber design. They won't need as much octane, and will tend to deliver just a little more power at cruise and low throttle.
As far as intakes go, if you really want power, don't mess around. Take advantage of the modern technology that's gone into intake design, and get either a Weiand Stealth, or an Edelbrock Air-Gap RPM. There is no downside to running one of these manifolds, and they just flat out work. Check your hood clearance. Early 'Stangs are a bit tight in there. All that said, your stock intake and carb would be great for up to around 250 honest horsepower, easy, and are a very solid streetable combo.
Once you get your engine up above that power level, you might have to think about going with a different carb. Your amazing old Autolite will struggle to supply enough air for your engine on the top end, though it would continue to deliver awesome throttle response and torque all the way through. It would just steal horses on the very top end. If you get to this point, I'd look at the Summit M-series carbs, which are a direct descendant of the old 4100, but a little easier to tune. The 600 CFM version would be perfect. Note that I am being very specific here: a 600 CFM Holley or Edelbrock carb would not do nearly as well. Why? Annular boosters, with their superior atomization even at low flow. The usual boosters in a Holley can deliver the same top end, but will never deliver the crisp throttle response or economy of your old Autolite's annular boosters. Edelbrock DOES have a new model that offers annular boosters too, but the price, performance, and "gee whiz, this thing works great right out of the box!" factor of the M-series carbs is phenomenal. And they're cheap.
Lastly, flat tappet cams work fine. They can be great, even. But if you drive your car a lot and don't want to worry about things, you need to really consider going to a roller cam. Modern oil lacks ZDDP, which is flat out necessary for a performance flat-tappet cam. It helps prevent wear, despite high valvespring pressures, and the intense sliding friction of the lobes against your lifters. Without enough ZDDP, a stock cam with gentle valvespring pressures is even at risk. A rowdier cam with stiffer springs, getting run to higher RPMs makes it very likely that you'll lose a cam lobe or lifter eventually. You can combat this with additives, or by buying special oil, but in my opinion, once you've gone down the road of modding your engine anyway, why would you stick with a flat tappet and have to deal with all this?
There are roller cam retrofit kits, and a good machinist can even allow your block to accept a roller cam, but all of that is rather expensive. IMHO, it's a lot easier (and cheaper!) just to start with an '85+ block that's set up with a roller cam, stock. There are very few differences between Windsor blocks all the way from '66-2000 when they stopped using them. 289-302, all the same, effectively.
If you're not running the GT40P heads, get a good set of Tri-Y headers with 1 5-8" primaries, and a nice thick flange for good seal. When it comes to exhaust, scavenging is the key. Pulses of exhaust help draw the next intake charge into your cylinders, when your engine's spinning at the right speed for it to happen. With unequal length exhausts, you don't get any real effect from scavenging. You just want to let the burnt gases out as fast as possible. But with a good Tri-Y setup, you get a modest boost to performance around 3k, and another on the top end. They also happen to fit pretty well, even in manual -transmission cars. They work great for street use.
Full length headers give no benefit to low or midrange whatsoever, except that they probably let more gases out (just like any unequal length exhaust). However, up around 5500 or so, they kick in with a single very strong boost to your engine's torque, extending your top end pull. Sort of like the cam overlap situation, they are king when it comes to peak horsepower, but mediocre for a street driven car. If you have trouble with traction (which is often the case in a lightweight Mustang!) this might not be a bad thing at all, limiting your bottom end, while allowing you warp-speed top end. If you're going with a mild build, however, the extra shot-in-the-arm that the Tri-Y's give, combined with ease of fitment, make them the better choice most of the time.
Now that you're blown away with the shotgun of Windsor performance knowledge, decide how much money you want to spend on this project, and multiply it by about 3, because that's how much it will really cost you.
Best wishes! =)
