They CAN. The 2.5 motor that you have (in 1985, has the automatic tensioner and some other minor upgrades) is offered in a 2.7 version and a 3 liter version. The difference in the 2.7 I believe is a change in bore size, but the 3 liter I believe has a different crank and has both a different bore and stroke. To be completely honest, with the money you're looking to spend on increasing the bore size, you MIGHT be better off actually looking for a used 3 liter or 2.7 liter motor.
The 2.7 liter is a very easy, direct drop into your engine bay, but it's also a 16 valve motor (where as yours is an 8 valve). You should be able to take the block though and bolt the single 2-valve cyl head right onto it...
I would verifiy this at www.RennList.com
www.944Online.com also sells parts for the car, so they should be able to sell you a stroker kit (so you don't have to do any real custom stuff)
The 2.5 motor is extremely expensive to modify (internally), and it doesn't yield that much more power. If you consider that it's only a 4 cyl, only 2.5 liter displacement, and it puts out 160hp... that's significantly more than most Japanese and American motors did in the 80s. For example, a "HO 2.8 liter V6" from GM only put out about 140hp... and that's more displacement, but less horsepower. Porsche did a very good job of tuning that motor.
If you're just looking for more power, I would also consider converting the AFM (air flow meter) system to a "MAF" system (Mass Air Flow). A bunch of people have been doing this... replacing that "barn door" late 70s technology with a Ford Escort MAF, and it's been yielding about 8-9 horsepower right off the bat. It's also BETTER, because it immediately yields itself to more horsepower on engine improvements (without necessarily needing an ECM retune).