New shifter feels mushy in 2nd and 4th gears
 

I just installed a tri-ax shifter on my T45.

Shift stops were set correctly, and the plastic bushing was in place. Shifting into 1st and 3rd gears feels very solid and crisp, but 2nd and 4th feels a little mushy.

Any idea what could be the problem?

From my experience all aftermarket shifters feel weird when first installed and then smooth out and get better after a bit of driving. If everything is installed correctly I would not worry about it.

I removed the upper and lower boots, and it felt nice and crisp in all gears. I put the boots back on, making sure they weren't interfering with anything, and the mushiness in 2nd/4th came back.

Yeah, I'm not worried about it anymore. I have bigger fish to fry, namely figuring out why ATF is spraying out of the vent tube and shifter at WOT.