Will a newer T5 Tranny fit a 66 with 289?

[bmxmon]

You sure can, it has been done plenty. That is also a good year for the t5 trans. I cant remember off the top of my head if the clutch from your 66 with work with the t5 however. When I was doing mine (going a completely different direction now) I bought a special flywheel that accepted the late model clutch for the T5. Though I would see if the clutch/pressure plate assembly will bolt up to your original flywheel first.
Anyway here is an article that should help you: Manual Transmission Conversion - Five Gears Of Freedom

You should post up some pics of your car! It'll be nice to know that sheetmetal for these cars is cheap!