I just mounted a 55lb 48" shaft Terrova w/ Ipilot on my boat in Oct. Yes, you do have to make sure there is sufficent clearance for the shaft when deployed. I used a socket that was 1 1/8 -1 1/4" long as my spacer so i would get the right clearance, and it worked out good for me on my tracker pt175. you will probably have to drill new holes as the old TM holes and new mounting holes probably won't match up. The lower unit will stick out beyond the leading edge of your boat in all probability as well, and watch out for the head unit. It could stick out beyond the side of the boat if you're not careful where you place it as well. I covered the front of my boat with painters tape since its painted to avoid scratching the paint when I was piddling with it and how I wanted it to mount.
After you get it placed on the boat, make sure the lower unit will clear the front roller, etc., when launching/loading BEFORE you drill the holes. you may need to upgrade your primary wiring if you don't have 24v now. GL
GO BIG ORANGE !
I meant to behave, but there were just way too many other options available at the time.