Maybe I'm on the wrong track here, but I don't get your point.
If I modified my phone beyond the stock possibilities as you did (rooted, custom font - in any case bootloader untouched) I would completely reset it to stock rom before handing it over to the repair center - because I don't want to discuss whether my modifications caused the defect or not. I guess that's a pretty common approach.
Now what is the point in rooting the phone, installing a custom font and then flashing stock, but only kind of half way without losing the modifications? Sony repair center will for sure be able to detect your modifications then, so you could save yourself from the stock flashing altogether and simply delete your private data before handing it in.
Ready for an adventure? Come on board and find out...
(no sailing experience required - feel free to ask me for details or check out the homepage)