I had the same issue in both my Toyotas. My 86 Pickup and my 94 4Runner. The fuse blocks under the kick panel kind of loosened up. I mean the contacts seam to get kind of loose and make bad connections. I replace the charge relay and I still had the same issue. I started messing with the fuse block and got it it pop on and off. So I went through and cleaned and bent the contacts back to closed and then lubed all the bare contacts with copious amounts of dielectric grease. Never had a problem since, Something to maybe look at if the relay thing doesnÆt pan out.

Also for the relaysà U can open them up usually what happens is that the contacts burn over time and they soot up to the point that they can no longer contact. Some times depending on how it is made you can take a business card, spay out the relay with contact cleaner and rub the business card though the contacts and it will be just abrasive enough to clean off the insulating corrosion and soot. This worked for me on headlight relays and such I never opened the charge relay but I would bet that its standard Toyota design.

Just something maybe to try may save you some bucks.