Hello Clois,
I've driven both with various degrees of 427's, 428's, multiple stroked 351's of different potentcy and the TKO is by far better for all around comfort and drivability. I have the TKO with the .68 overdrive 5th gear in my car. The TKO II has a .83 overdrive 5th so adjust the figures below accordingly 32% vs 17% reduction in RPM when going from 4th to 5th.
If you are only going to drive your car on the track the toploader is the choice for gear selection and bullet proof nature. If your planned driving includes driving/cruising for pleasure the 5th gear is great. Last weekend I drove my Unique 427 to Redding 220 miles cruising on the highway 75-90 MPH most of the time in 5th and occasional drops to 4th and got 15MPG.
The engine has a tremendous amount of torque and in 5th will accelerate very well, if you really want to move fast the down shift to 4th will clear the road in front of you. Cruising in 5th at 75 the engine is turning 2300RPM at 100MPH it is turning 3000 RPM. In 4th at 75 MPH the engine is turning 3300 RPM and in 4th at 100 MPH the engine is turning 4200 RPM. you can have a conversation in the car with no problems and minimal yelling.
BTW I have 3:54 gears in my rear end ....this is a factor. I owned an SPF with the 460/535 ford crate motor with the TKO and 3:73 rearend gears in it and had a very similar experience. I put the TKO behind the stroked 351 that is in my coupe with 3:55 gears in the rear end. Drove the SPF 10,000 miles and the Unique 4000+ miles...the FFR Coupe is still under construction.
I'm sure you will get numerous responses here but, make the choice that fits what you will be doing in your Cobra.
Tony R.