The better engine options on these cars included a 260 cubic inch V8. By the time the "real" 1965 models came out, the engines were upgraded to a 200 cubic inch straight 6 and a 289 cubic inch V8.
The 1965 model saw the replacement of a DC electric generator with a AC alternator. The 1965 models have a light on the dash that says ALT instead of the GEN that was on the 64 1/2 models. The Mustang GT was introduced in 1965, and only moderate design changes were made for the 1966 model. One option on the 66 was a AM/FM Monaural radio, one of the first available on any car.
There are obviously a lot of Mustang collectors out there, and the early years are still very popular. If you are building one, or looking to buy one, I suggest you check out the listings on eBay before making any big orders from the likes of JC Whitney. I'm not saying they are a bad company, but you can often get used original parts on eBay that will work better than any new aftermarket parts, and they'll do more for the resale value. I also encourage you to read up on what parts were original on your Mustang.