Shuttle-A can dock with enough clearance... previously the engines would not fit without penetrating the aft bulkhead of docking bay , but by a very small margin.
I pushed a bit the dock (after rework) and had some hope when you talk about "small margin" but I tested and the margin is in fact enormous.
I would require to push gears, front hovers and rework almost all the bottom, so no chance, sorry. Would be much more simple to make a shorter version of ShuttleA.
That way, we could maybe create "orbiter geology", collecting different rock samples, allowing for surface EVAs to be focused on doing scientific work, like Apollos 15-17 were heavily focused on the lunar geologic work
One can make scenario where rock are already spawned ready for grabbing/pack but for active module that spawn rock I'll leave some work to other author.