You could get a cold air intake where the filter lives inside an enclosed insulated box to shield the hot engine bay air from the filter. You may get a little extra performance, but that's negligible, and usually not worth the cost. Looks cool, but that's about it.  Any other kind where the filter resides in the engine bay exposed is a waste of money.

Any other "large scale" upgrades are possible. You can go as mild to wild and are limited by your wallet/budget because to do them properly it won't come cheap.   

Realistically, it would probably be a lot cheaper to sell your current Stang and find a decent used one with a V8 and manual. Getting substantially more HP out of a 15 year old V6 would be both expensive and likely to compromise its reliability.

So my first instinct was to say sell it and get the GT as you will save a ton of money over putting work into the V6. However, I saw that you have sentimental value to the car and I can respect that. 

The next question I have is: what does your budget look like? An intake alone isn't worth doing. Let me give you some options:

1. Keep the V6 - In this case, you would be looking at an intake, exhaust, rear gears, and a tune. At that point you would be still considerably slower than a stock GT and into the car for about $3000. Mind you, I also don't know what your end goal is (Track car, strip car, cruiser, etc.) so this may not even be an option. Total horsepower gain would be in the 35HP to 45HP range.

2. Swap in a 4.6L 3V V8 - Same engine as the GT. May as well swap in a Tremec T-56 while you are at it. If you currently have an auto, that process is going to suck. Of course, you still need rear gears, a better axle, carbon fiber drive shaft, better cam phasers....may as well throw some Mother Thumpr cams in it while it is out, add an intake, upgrade all the harnesses and electronics, get better tires.....you go that route, you're up around $20k - $25k installed. No reason this setup shouldn't make 350HP with a nice 93 octane tune.

3. This is my favorite: I call it the "Go For Broke Special", cuz you're gonna be broke if you go this route. BUT...you will have an animal of a car. Fully built 4.6L 32V V8 out of a Terminator Cobra, fully forged, Kenne Bell blower on 18 psi, all new everything front to back, top to bottom. At this level, I'm talking serious chassis reinforcement, a fully built Tremec Magnum XL transmission, custom exhaust....The Works basically. This kind of setup....looking at the 850HP range. BUT...also looking at $50k to $60k installed. 

As @Toyotagrl said, it all depends on your wallet. I make things go very fast for a living. But none of it is cheap. I have a 2004 Cobra coupe shop car that has a twin turbo setup pushing out 1500HP. I also have over $100k just in parts in that car. So the things you need to figure out are:

1. End goal - Cruiser, daily, track car, give people nightmares car

2. Budget - Be realistic. If you want significant power increases, it doesn't come cheap. Realize that you can write off $15k to $20k just to swap the motor and trans. And guys who do it cheap use junkyard parts and don't do it to factory spec. I'm talking about installing it like I would at my shop where I warranty the work. Different animal.

So I say think on it, decide if it is worth it to you, and go from there.

Realize one very important thing: at the end of the day, the VIN will always be for a V6. So you will literally never get your money back out of it. Only put in what you can afford to set on fire because it is gone once you spend it.

Another question for our expert @Mod_Man.