AFAIK, the MIM Standard comes with ceramic magnets. Usually the ceramic pups have a easily visible bar magnet (or two) on the underside of the pup, Alinco pup's don't.
There are MIM's that come with Alinco pup's, but these are usually special editions/re-issues etc..
http://forums.fender.com/viewtopic.php?f=6&t=71072
Before you swop them out, have a think about it - I reverted my MIJ back to it's ceramic pups a while back (albeit a very odd looking set with metal baseplates) and I'm rather happy - even after play testing against a range of MIA's.
One thing, I had a load of work done of the wiring - everything upgraded, mods (treble bleed/K7) and there was definitely a difference pre & post wiring.