No manual transmission exists for the current (E70) platform.

(Assuming US-market) Both the 3.0si and the 4.8i engines are mated to a ZF 6 HP XX TU (where XX is either 19 or 26) electronically/electrically controlled automatic transmission. They are essentially the same except for the final drive. The 3.0si (ZF 6 HP 19 TU) has a final drive of 4.44:1 and the 4.8i (ZF 6 HP 26 TU) has a final drive of 3.91:1.

With regards to fuel economy, neither transmission will increase or reduce consumption. Engine size should be your focus.

Someone else can chime in on the 35d.