The most important thing is that you backup your entire database as well as your entire quests directory before making any changes. I always keep multiple previous backups just in case. It is a good idea to store the backups on a separate drive in the case that your current one fails.
As for updating to PEQ when you have a variety of custom content, I think your options are pretty limited. Some things are easy to update, but others are not easy at all.
You can update your items table by simply making a dump of the PEQ items table and then remove the top part that deletes the table and recreates it. Then just source that table in on top of yours and it will error for all that already exist so it doesn't overwrite any customization you have done to current items or new items you have created, but it will add in any that you don't currently have in there already.
You can also update other tables like the AA related tables without having to do anything special at all, as long as you haven't customized it at all.
For updating spawns and loot and such, that is no easy task. This is because you will run into issues with NPCs spawning that you may have deleted, or spawn points or loot drops or whatever that overlap what you already have set. I don't know of any way to update these smoothly, so I just leave them as they are. I don't personally care about non-custom zones on my server, so I could care less if they are updated or not.
You should also be able to update tradeskill tables if you don't have any custom recipes. Pretty much any table that you don't have custom stuff in should be ok to do a normal update on.
For quests, download the quest directory and delete out any folders named after zones you have customized, and then just copy the remaining ones into your quests folder and let them all overwrite the existing ones.
I am sure more updating is probably possible, but this really isn't anything that can be done easily or cleanly without a considerable amount of work to get things back to normal.
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