Hi Tim,
First let me say that I sympathize with having to deal with this issue. I know how fustrating these kind of things can be. I've had many years of experience with Pentax AF macro lenses, both their 35mm ones as well as the 645 FA 120, all with focus limiter switches. If I understand you correctly, even when you have the lens "in hand", not mounted on the camera and in manual focus, you cannot turn the focusing ring any closer than approx 3 feet? If so, my guess is the limiter switch may be broken internally and so when you move it externally (even though you might hear a click), it's not engaging/disengaging whatever internal mechansim it's supposed to. I cannot imagine it being a difficult or complicated fix for a qualified tech. It may need a small internal part replaced or it just may be something moved out of position internally and has to be repositioned.
Pentax has a 3rd party official repair facility here in the U.S named "CRIS", where they are able to get original parts for repair assuming they are still available, which should be the case for the 645 FA 120 macro. There are many other good repair individuals who can probably work on the lens too.
I would assume you purchased the lens 2nd hand and weren't aware of the problem till now? Reason I ask is on the outside chance you purchased it new, it would still be under warrenty. I cannot think of anything off hand to receommend trying unless there is additional observations regarding the problem.
Keep us posted on developments and hope it gets resolved soon.
Dave (D&A)