There is no reason you can't use the TR3 clutch if you want to. I ran that way for a lot of miles, no issues with the clutch. I only swapped clutches later because I wanted to use a flywheel that was already drilled for the later clutch.
If you do want to use the later clutch, then you will have to change all those parts, plus the TOB carrier. Be sure they add the dowel pin holes to the flywheel as well as the 6 tapped holes. Any error in the location of the pins can cause vibration later on.
There are several ways you could go on the clutch slave mounting. I still have mine mounted TR3-style, with the slave bracket on the back of the gearbox flange. Since the TR6 flange is thicker than the TR3 was, that moves the slave slightly closer to the operating lever; so I shortened the pushrod enough to allow adjustment in the usual manner. I also made a little tab to connect the spring (to keep the tension about the same).
Another option would be to beat the flange flat on the cover that goes on the front of the gearbox, and mount the bracket there. I think the brace is threaded enough to fit; and that if you then mount the slave ears on the rear of the bracket, the resulting location should be just about right (within the adjustment range of the pushrod). But I haven't tried it.
PS, the length difference is only about 3/8". I drilled new holes in the cross member that just touched the old holes and used flat washers plus lock washers on the bottom. Also had to bend down the flange on the back of the cross member; but that may vary.
PPS, the extra length also moved the speedo cable back in the hole through the floorboards. I added a piece of slit fuel hose around the cable for protection. Here's a shot where you can see the bend in the crossmember and the hose on the speedo cable housing.