My memory is a bit fuzzy (was a long time ago for me), but there is at least one bolt hole that does go unused. They added a "dowel bolt" to the TR6 setup for better locating (I guess) and the TR3 block doesn't have the hole for it. What I can't recall for certain is whether there is another unused hole over near the starter.
Two more look unused, because they hold the locating dowels. On the TR6, these were replaced with "dowel bolts", which are bolts with precision diameter shanks that double as locating pins.
Barry's photos do show bolts in place of the studs; probably because that's what his PO used. Probably work fine, if you get the bolt length just right. But the holes are blind, and as I recall, not overly deep. So if the bolt length isn't quite right, you'll get either too few threads engaged in the block, or the bolt bottoming in the hole instead of clamping the gearbox flange to the block. The studs seemed preferable to me.
Here's a shot of mine, where you can see the empty hole, and the 3 studs across the top. The apparently empty hole lower down has a dowel in it (retained with a drop of Loctite).
56 TR3 TS13571L daily driver
71 Stag LE1473L awaiting engine rebuild
7? Stag awaiting gearbox rebuild
Just to be sure I got it right
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