4Runner hard shifting

I recently swapped a 97’ 4Runner Limited trans into my ‘02 Tacoma for 4wd purposes. I was under the impression that the donor trans was otherwise in good working order. I replaced the fluids to spec and double checked all lines, cables, etc. I’m still getting “jerky” shifts out of 1st gear intermittently, primarily at low speeds. My fluid levels have remained fine and there is no discoloration. Is this cause for concern or do most of these older 4runners have this issue?