I think the '65 Shelby engine mods also ought to include the side pipes with glass pack mufflers and no cross-over. I'm not sure if this mod was a horsepower adder or a horsepower subtractor. Another power-related mod was the hood scoop. Some sources also mention a dual-point distributor.
Shelby also swapped out the factory toploader for a Borg Warner T-10, removed the back seat, and added overrider traction bars. A 3.89:1 gear was standard, with a 4.11 a no-cost option. Both ratios came with a mandatory Detroit locker.
Removing the back seat would subtract a few pounds. I don't know if the T-10 subtracts weight or adds it. I don't know the effect of a T-10 on rearwheel hp either. The traction bars and gear would definitely help in the quarter mile, and the locker might also help. (I'm not sure if lsd really helps ET's with such low output engines.)
Speaking of output, a GT350 tested by Car & Driver in May 1965 trapped at 95 mph, which with a 3030 lb as-tested weight calculates as 202 rwhp, 253 fwhp. (rwhp = weight x (trap speed/234)^3.)
Whatever the output of the '65 GT350, no one had more experience or success with the Ford 289 than Shelby American. The regular production 289 Shelby Cobras had been running a K-code 289 with the same mods as the GT350 got, since '62 or '63. In racing form, 289-powered GT350R's, Cobras, Daytona Coupes, and Shelby managed GT-40s won just about every series in which they competed.
The kids' '65 at Marin headlands 1-9-05