The power lost through a jackshaft system will be insignificant. As will the change to the handling of your kart from moving the seat struts.
I don’t want to sound mean but if you were competitive enough for any of this stuff to make a difference you wouldn’t be asking these questions.
Bolt the thing on and go run about a zillion laps, that’s what will make you fast. Talk to the other guys at your track who seem to know what they’re doing. Test, Test, and Test some more. Keep detailed notes. Swap karts with anybody who’s faster than you and see how their set-up feels.
I can understand your desire to get everything just right but it’s not gonna happen before you get your kart out on track the first time. LO206 is designed as a beginner/sportsman class, a place to learn and you learn by doing.
Go get yourself a BFH, a 2×4, a set of bathroom scales, a measuring tape, a stopwatch, notepad and pencil. That, lots of pump gas, oil changes, tires, and determination are all you need to master this.