Redneck mathematics shows the weight of the engine, trans, clip, and radiator should drop the suspension about 4"
I have lots of hours building inner fenders on my truck. They are not pretty, but you can not see them under the fenders they are attached to unless you remove them and set them on the floor. Mine are completely removable from the fenders, with the fenders bolted in place. They do what they are suppose to do. I suggest you install everything you need to have installed before you concern your self with the inner fenders. Make it run and drive first! Then, after everything else is done, cardboard (beverage containers) will be your best friend to patch together the inner fenders. You can cut, tape, and staple a pattern together then transfer the refined cardboard pattern onto pieces of steel you can weld together, and hold in place with screws. The purpose of the inner fenders is to keep the engine compartment free from road trash. They are hidden under the body, pretty is not what is important, function is.
Also obviously need to lengthen the prop shaft 10". Makes total sense because the trucks wheelbase is 10" longer than the miata. Inside isnt terrible. I lost the heater box and most of the duct work. The coils will need to be relocated from the back of the engine to the firewall. And the heater hoses on the engine need to be re routed, I think there is a coolant reroute upgrade kit available that may solve my issue there.