Make sure your heater valve is closed. The slide lever should be at the
clockwise limit. You can also touch the two rubber hoses on the right
side of the heater to confirm the valve is working in the off position.
They should not be hot.
I echo what others have said about having the transmission cover
sealed. I had a problem getting a good seal over the arch in the
bulkhead. The carpet on the bulkhead goes over the tunnel. Mine was
difficult to get in place. You might test this by putting the car on
stands in a dark garage, get a helper to move a bright light around the
bulkhead, and see if you can see any light while lying under the car.
You can also replace the underlayment below the carpet with heat shield
padding. Moss shows a roll for $29.95 as an example (page A5 in my TR6
catalog). I've seen a similar product locally for about $20 a roll. I
know people with modified cars that use this to keep cool.