My current TR3 also had a block of hardwood on the clutch pedal when it came to me; although the PO had just drilled the existing pedal for flat head bolts instead of using a U-bolt.
You might look into various small changes that would raise the point where the clutch engages. On both Stags, I found a fairly severe amount of wear at the point where the MC pushrod joined with the pedal. I wasn't willing to pull it all out to fix it properly, so I reamed the holes oversize and used a metric bolt (8mm IIRC) in place of the clevis pin. That gained me over 1" at the pedal.
The TR6 uses a plastic line from the clutch MC to the slave, which swells under pressure and effectively loses motion. A hard line plus a short length of flex line (like the earlier TRs use) would regain that motion. Or I believe several vendors (including TSi) sell a "braided stainless" line (actually teflon inside, the braid is only for abrasion protection) that also flexes less than the original line.
The larger bore MC used on 69-70 TR6 would also help, if you have the later one.
Yet another option might be a longer pushrod for the MC (so the pedal is higher at rest). I vaguely recall seeing adjustable MC pushrods for sale, but don't recall where offhand. Worst case, you may have to fabricate something.
Might also be worth double-checking that the springs inside the slave & MC are in good condition. The MC spring on my previous TR3A was broken into 4 pieces by the time I figured out the problem.