When you have the settings set to pre-re you need to make sure you download a data folder that is also pre-re, for both item translations skill translations and maps like izlude,
the for izlude just download the old izlude and put it in your data folder / grf
As for the mobs in 2007 I remember that orc zombies where not that strong and could easily be mobbed and killed in groups even before your 2nd job.
To answer your overall question will there still be issues, I'm sure there are small ones here and there but most are caused by using a non pre-re grf setup, with a few of the renewal npcs leaking to pre-re
For your woe question I wouldn't know off hand I'd have to look into the npcs bit I'm on phone