codel529-
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Not sure if you've already found your answer but swapping the linkage is not an easy task unless you've done it before. The most difficult part is finding a custom-made drill bit that can keep the proper bore ID for the shift rail seal. Otherwise it will leak continuously (like what mine is doing).
Because the MR2 has the engine behind the cabin, and the Matrix in front, the shift linkages are on the flip-side of each transaxle.
I advise instead to find a Matrix-native C60. It is a six speed version from the XRS model and will be a direct swap. The 6-speed C60 from the Corolla is preferred over the 6-speed C60 out of the Celica GTS / Lotus Elise/Exige because the Matrix C60 has a 0.725:1 6th gear instead of the shorter 0.815:1 6th gear in the Celica/Lotus. Take a look at the ratios and discussion posted here:
http://bigmike.marlincrawler.com/forum/index.php?topic=45I don't have personal experience with converting from a C59 to the C60, but if it isn't a 100% direct swap than you can be guaranteed there are parts that make it swappable by using XRS axle shafts and/or hubs (and/or brakes in the absolutely worst scenario). Your 1ZZ has the same bellhousing bolt pattern as the XRS's 2ZZ engine.
With the 6-speed, you'll have better acceleration 1-5th gears and the taller 6th gear ratio will yield better fuel economy on the open road.

BigMike