I agree, the only good reason to do it is to clean up the congestion in the engine bay area around the oil fill tube (plug wires, fuel lines, oil fill, throttle body, all in same area) or to be able to use parts that are much more available (bigger throttle bodies, blower discharge tubes, etc).
You can't run a strut tower brace without modification
Only reason people claim a better throttle response is because of the cam shape the cable rides in on the throttle body. Fox throttle is very touchy and when I got my '95 I found it easier to drive slower through parking lots, etc due to the pedal not being so touchy.
As far as ISC valve, they are swappable. A '94/5 will fit on a fox and vice versa. I personally don't like how the fox ISC wire plug faces down and touches the valve cover.
I have ran TrickFlow valve covers with my '94/5 cobra intake and no spacer and currently run fox valve covers with no problems at all.