Of course they can't locate an aftermarket SJB, that a Ford only part, there is no aftermarket SJB, what are they thinking (other than they don't actually want to replace it because that costs them money)??? No idea if they can successfully clean it; the right way, assuming there actually is a water leak, would be to find and fix the water leak and then REPLACE the SJB with one that hasn't been wet. Due to age, a JY SJB may be the only option, I don't know, I haven't looked for a new/reman one from Ford. It is true that the HVAC unit intake is in the general area, but it's up higher. IMO, the story you are getting about humid air, and so much of it, and to the point that it's literally raining in there and causing the problem sounds rather flaky and near BS, Ford would have had warranty problems clear back in 04 if that were the case and they would have had to address it.
If it's leaking you can look in there for yourself and see either current water after it rains or streaking and or mud on the bottom of the SJB cavity. If this pans out then IMO, they may be giving you a line and a low $ fix just to get it past warranty. After all, the vehicle is 12 years old, things do happen with time.