You'll also need to slot the holes where the rear mount attaches to the cross member. The 4-synchro boxes are around 3/8" longer through the mounting points.
Depending on the vintage of TR6, you may need longer mounting bolts and some adjustments to the clutch slave mounting. I have a later TR6 box and had to shorten the clutch pushrod to make it fit with the slave in the original position.
The shorter input shaft does not seem to be a problem. Still, it wouldn't hurt to replace the pilot bearing while you're in there. Make sure the locating dowels are in place as well.
Don't forget to wire and test the switches before buttoning it up. In retrospect, I wish I had just replaced the one that acted a bit funny instead of just taking out the shim.