I've been getting into the habit of taking refractometer readings while sparging but I usually just sparge until I have the preboil volume I'm looking for. Granted, I fly sparge. It sounds like maybe you're batch sparging? It depends on your kettle, burner, boil vigor, wind, etc but your boil off should be fairly consistent from batch to batch. I usually calculate recipes at 6gal post boil and plan on leaving a few quarts or so in the bottom of the kettle. That being said preboil is about 7-7.25 gallons.
I have to say though, nice work MacGyvering your way out of that one. I don't see any reason for off flavors because of the boil. Maybe more caramel flavor? If you were fly sparging, I'd be more concerned about an extra long sparge and ph issues.