While it is true in general that an excellent condition un-modifyied mustang will be worth more on the market than a modifyied one, you sometimes need to examine exactly what the difference in price is.
Case in point:
http://cgi.ebay.com/ebaymotors/ws/eBayISAPI.dll?ViewItem&item=2467184732&category=6236
Started life as a 6 cylinder and its over 20k....(in case you are wondering this car caught my eye because of the amazing similarities between it and the Death Trap in my garage)
With that said....
It is your car, you have expressed a strong feeling of keeping it forever, do what you want, collect all the advise you want, but ultimately YOU make the choices, do what you want.
If you heavily modify your 6 to get a lot of power out of.....with some moderately priced parts you should be able to get at least 1.2 HP/Cube out of it and with some pricier custom work with turbos you can get a lot more but all this stuff "modifies the car" and it is no longer original.
So I say, if you want an 8 make an 8, MCA concourse and therobred (Spell?) trailer division all have other sporty anc fun cars to drive because they can't/won't drive their mustangs. I look at it in much simplier terms, as long as your not cutting out the shock towers, or tubbing the rear end, etc...anything you do to the car is revesible....if you put the v8 spindles, rear, tranny, brakes, suspension on the car you have made the car safer and more reliable even if you still have a I6 in it

.....then you can add the v8 too and have alot more power on hand. Just put all the parts you remove in a box and stick it in the attic....if heaven forbid you need to sell the car one day..you can sell it as a modified 6banger with all the parts still available to do a full concourse restoration

(might even make more than market price then)