I think that the current market has proven two things.
1. You can modify a Mustang and sell it for a profit
2. The Mustang, stock or modified, STILL appeals to alot of people.
Personnally, the modifications should be well thought out, and PROPERLY applied. Most modified cars that are bringing big bucks have been completed in professional shops not backyard garages. I, however, plan on putting an Air Ride Technology four-link suspension, stroker motor, and some other mods to my next project. So I say "go for it".
One last thought... are you thinking of making these changes to sell the car for a profit or please yourself? If it's the latter do what will make you happy.