Well, I've built a jaguar and technically it worked out a fair bit cheaper even after the modifications.
Unfortunetley all the unseen and unexpected costs (import tax, professional assembly) drove it up to about the same mark as modifying a shop bought one.
So if you go the right way about it (don't mix US and jap bodies and necks, wait for good deals etc) you can get a more personal mustang cheaper that way.
The main probs you will have are finding a Mustang body and a 24" neck, ebay will have a good number of these but its a matter of winning one and paying a good price.
I had the most awful time finding a neck for my jag after getting a good deal on a body, I ended up trying three necks then I cross bred the Jap body with a 67 Mustang neck that needed professional modding.
Cost quite a bit more than I had planned in the end, but I do love my zangy new/old Fender Mustaguar.