With the simple use of countersunk flathead allen screws to replace the 4 waterpump pulley hex bolts, you gain 1/4" of clearance. They have not come loose in 20 years. Another thing that increases clearance a bit is to remove the shims from the ZF mounts in back, loosen the motormount bolts (ALL of them) and lift/pry the whole powertrain backwards, using the sloppy fit drill holes to their maximum.Then use washers to reshim the rear ZF mounts as necessary. That gains another 1/8".
The actual bulkhead 'reduction' using your stock panel is combined with sawing the bubble part of the big panel free. Being leatherette covered thin fiberglas, a wood saw or any other kind can be used. The bubble's upholstery is done by the factory as a separate part, so the saw-cut line goes in between the stock upholstery pieces. This semi-factory mod has been written up in numerous POCA articles, available from the Archives. Upholstered Gr-3 cars often had this done for frequent maintenance convenience.
Once done, the bubble/fiberglas section is usually held to the steel door with a few patches of velcro. The main panel can now stay in place forever while the bubble-only is pulled off for access to the steel door. For our car, I use only two steel door screws in the top corners- the door is not structural and doesn't need to be fastened that securely. Makes door access a matter of a minute or less and looks stock -if that's important.