When I built mine, I followed the Mugen instructions for setting up the two-speed clutch shoes. That is to screw your cap screws in the ends snug tight (don't overtighten) then back it out per Tamiya instructions. Then, you take the grub screws on the top and bottom and tighten each of them slowly until you see a very thin gap on each end where the cap screws are screwed in (see Mugen MTX-3/MTX-4 instructions from their website). Hope that this helps.
After do the above mentioned, the two speed shifted fine but you may have to back off the cap screws another turn or two depending on the type of track and where you need your shift point set.