Filter between the gen1 (<2010, 2010+=gen2) and speed are actually both cartridge style filter's "paper" as you called it guess what's inside the "normal" metal filter..the same stuff.
The 08 speed you have has had the spin on filter conversion done. To be the same as the gen 2 speed 3.
The engines between any of the speed 3 and ms6 are all swap able as they're the same (minis some improvements on gen 2 ms3).
I'm not too familiar with exact differences between the ms6 and 3 but it should just bolt right up, harness etc I believe to be the same too.
@Sho any differences in the ms6 bay be gen1 you're aware of?
Edit: naturally you need to use a speed 3 transmission for the 3, I know the 6 Turbo oil drain line are slightly different to clear their transfer case, and the 6 cold pipe of tmic is different too so you'll want the 3s one for that if you're tmic