[mickmate]

Good questions
1- Are the fenders supposed to be notched at the bottom or are holes cut in for pipes?
Originals used a hole through the body as they have a 3/4" tube wrapped in sheetmetal.
2- How much clearance is needed between fender and pipes?
I run about an inch to allow for movement on motor mounts
3- Pipes are flange fit, headers are slip-fit. Do slip-fit tend to leak more which is better?
Leaking isn't better but a good slip fit with some manifold seal goop works well.
4- Should I rubber mount pipes for vibration?
Definitely have some kind of rubber isolators, at the very least a pivot, or it can shake the car apart.
If you need any pictures or ideas let us know.