Yeah, you'll have to lift the rear of the engine some, mostly to get the gearbox out. The TR4 box is also longer by about 3/8", so you'll need to slot the holes in the rear cross-member. I would also add the reinforcement for the taper pin before you put the box back in. And, it might be worth making up some long headless bolts, to use in place of the studs, as a guide for installing the box.
Otherwise, it's pretty straightforward.
If you were using a later gearbox, there are also some accommodations required for the thicker bellhousing flange, but as I recall the TR4 box was the same thickness as the TR3.
Oh, and if your TR3 is before TS50,000; you may need to do some sheet metal work on the tunnel, to clear the starter bulge. You might also want to consider combining the top covers, so you can keep the dipstick.
Although the TR4 shift lever will work, my preference would be to keep the original TR3 lever. It will fit into the TR4 top cover, but it may be necessary to drill out one or two of the holes, so you can insert the cross bolt. At some point, it became two threaded pins instead of the early cross bolt.