As I understand it MIJ was used on older models of Japanese Fenders. Nowadays I understand they are all CIJ models. Never played a bad CIJ Fender. Having imported 28 Aerodynes and retailed them all with nothing but praise from the buyers, I can say that every single one was perfect in finish, construction and tone. They also made a special Jaguar bass for me that took 6 weeks to make and it is just superb.
Apart from that, I really cant understand why anybody in their right mind would want to 'F' about with the electronics of a Geddy Lee Jazz. Just why would you ? If its modded then it isnt worth as much as a standard model - and if you should wish to pass on in the future then you should be aware of that, and be prepared to either struggle to sell it or get less for it. Probably both to be honest.
However, the choice is yours, but I wouldnt give it the time of day personally. There are many others out there without issues. I'd go for one of those.
Theres my two-penneth anyway. Good luck.