To ease the checking operation, consider disassembling the shaft into three pieces. Each of the end sections can then be checked both in the forward location and the aft location in the chassis. Much easier to handle.
Re: centering sleeves, if the sleeves do not bottom on the transmission and rear end shafts before the bolt flanges capture the flex discs, there should not be a problem with sleeve protrusion length. The drive line sections should be able to move endwise when the flex discs are all bolted up.