I've some pictures to help you with this decision.
My original cover from my 1973 FJ40 is the blue one, stock with 3 speed shifter and tcase lever. I had hacked a hole for a PTO shifter in it when I added a winch.
I picked up a clean 4 speed cover (tan) and was able to compare the two. The 4 speed shift cane is centered on the cover, the 3 speed is offset to the passenger side (original design was for column shift).
You can see from the following pictures there is some sheet metal work to adapt a 4 speed cover to a 3 speed shift cane. The transfer case lever will work, but you'll need to get the four speed boot assembly to fit up to the cover.
I went with a fiberglass cover from SOR, and their gasket kit. Last picture.
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