After having discovered your DIY Manual and some experimentation, I have determined it is the Safana trigger/script with the randomization of the Manual of Bodily Health which is the problem.
First, I removed the Manual completely from the randomization tables ... no hang. Other items are randomized correctly, Manual remains untouched.
Second, I added Manual back in (as per your guide explains) but changed the reference of safana.fl in weidu_bg1item.2da (baf\flrsafan.baf appears to be the modified script dealing with her getting impatient and leaving? I assumed this must be the reference). Used container1 instead as was referenced in another list location for that same container ... no hang. Took me three re-randomizations before the Manual was not randomly assigned that same location, and experienced no hangs without it being present. Not sure what happens with Safana, however.
I'm not sure if the *.fl references in general are the incompatibility with the BG1 engine or just this specific case, as I haven't gotten far enough to test the later ones. Any way to verify this?
I can still provide the files from override folder, but i am guessing after this new information those won't be much help. Let me know.