If using a Ford 9" Rear-end in a hotrod build, am I limited to specific engine and transmission combinations?
Absolutely not restricted to any build. A 9" Ford rear-end is utilized in just about every kind of hotrod build out there, mainly due to its strength and longevity. You can find one made (built) for just about any application out there. You can even find them without any type of mounting on them where you can add your specific type of mounts for a specific application.