elm ver 1.5 works fine z series engine. although u need a code to let torque app identify the engine.
only part getting dirty INSIDE throttle body is the throttle plate, with passage of time the carbon deposits on edges and seals it better if it had a slight leak. Maybe the throttle plate might be little loose in ur TB which was sealed by the deposit which u cleaned of, this might be one reaons of rough or less smoother.
the RPM difference is too much, if its with auto txn, is the TCC locking up?
turning on the AC DOES increase the RPM from 900 to 1000, if there is no impact on RPM then either its not wired up properly or the RPM are already on the higher side.
I think, there is nothing to be tuned in EFI manually, just need to make necessary and timely maintenance, like changing spark plugs or checking if sensors working okay within range or not.
that too happens after certain thousand KMs provided no jugaar done with it.