Aviator in a Cobra

I am tierd of chasing ticks, taps and rattles in a 98k motor and am going to an Aviator engine " cheap and an 05 " . I need to hooke up my Tremac to this 6bolt. I am going to use the lid, valve covers and exhaust from the Cobra.... Am I missing anything ?????? Do I need to make any Mods ? Will it accept an 04 Mustang Gt flywheel? Do I need dowells? Let me know please I will be doing this change next week and I need to have my sheet together for the shop. Thanks Scott