Hard to say how you'll make out on power, depends a lot on the condition of each motor and what parts it has inside. There are a lot of TR3 motors around with 87mm liners in them, as for a long time the 87mm liners were cheaper and easier to find than the stock 83s. The 4A changes supposedly improved mid-range power (which after all is most important), but the peak power rating didn't improve by much (100 bhp to 104).
For your case (late TR3A), no changes are required to the tunnel or driveshaft. The slip joint in the driveshaft has enough travel to accommodate the slightly longer gearbox, and the tunnel will already clear the starter bulge.
Of course you'll need to add the wiring for the OD, but that is easy enough. I'll make one suggestion though : add a smallish fuse in the power to the solenoid. That way, if the solenoid somehow hangs up and doesn't open the contacts inside, the fuse will blow before the solenoid burns up. I use an 8 amp "slo-blo" just because I've got a box of them, but I believe even a 5 amp regular fuse will work fine.