They seem to be compatible, at least between the L/G/W trannys I have shifters for as well as with the newer trannys in the Tacomas. I combined a W56 shifter base, some parts from an old L-series 4-speed stick and a Tacoma short throw shifter on my W56 gear box:

http://www.4crawler.com/4x4/ForSale/ShortThrowTrannyShifter/index.html

There are a few minor differences in terms of how the shifter is held to the base and the spacing of the pivot pins inside the base.