There are a number of things you can do to your car to get the power you want without breaking your bank. I will offer to you here the most obvious options you have that exclude boost and nitrous as I beleave both have significant tradeoffs (namely reliablility for NOS and fuel mileage for supercharging). This list takes into account the fact that there is little to no room for your engine to get taller. That may explain the cost of your supercharger setup, being as it has to be specially engineered to fit under the hood of your TC AND still live in harmony with the other belt accessories you currently have.
- PI Heads
No, PI doesn't mean "Police Interceptor." It actually means "Performance Improved" and many Mustang guys have reported seeing break horsepower numbers in excess of 300HP in their upgrades. I don't know when they became standard equipment on the Mustang but I think you can find them on anything made after 1999. PI heads also require that you install the PI intake as well, or they won't fit. You should be able to find these parts in any junk yard at reasonable cost, especially if you know how to haggle with the guy at the counter. Add to the PI heads a set of mild upgraded cams and you'll have an engine that breathes much better than what you have now.
- Exhaust
Upgrading to a modern high flow exhaust with mandrel bent tubing will likely help you gain significant horsepower at a reasonable cost. For you to replace the whole thing with high quality headers, high flow catalytic converters, and an X - pipe you're looking at $1500. If you're worried about the exhaust of your car being too loud you will probably do well by using the stock mufflers off an 01-04 Mustang GT.
- Shorter Rear End Gears
You do already have a 4R70W transmission, but changing your rear gear to something in the ballpark of 3.50:1 will improve your off the line accelleration without putting your fuel economy in the 22 MPG range. You'll also find that you have better highway acceleration without downshifting. This is also by far the least expensive modification you can make to the car at a cost of less than $200 for parts.
- PCM Flash
Any change you make to your engine or driveline will require you to re-flash your PCM. This will allow you to not only optimize drivability by tweaking fuel and timing curves, but also tailor your EGR for some improved fuel economy. I don't know what this would cost to do, but if I payed more than $300 for it I would feel ripped off.
Any one of these mods will improve your power, but using them all in concert could yeald you significant power gains. Uprading the heads or exhaust will easily put your torque number over the 300ft-lb mark, which will really help get that 4000# hunk of steel movin. Honestly I don't think a supercharger is the best way to go to hot rod your Lincoln. If you want to go with boost I strongly recommend the use of a turbocharger as you will see significantly less fuel mileage loss for your performance. I do feel though that the most pleasing torque curve for you is going to come from a setup that does not include boost.