I need to run some wires under the car, i bought some push in zipties and was going to drill some holes but not sure if its a good/safe idea drill into these "body rails" or whatever theyre called. They are shown in the body alignment section of the FSM.

 

Why not put the wires under the rug next to the door like the factory does and is common practice everywhere.
The engineers who designed the car know what works and what does not

 

Those are frame rails and are, for the most-part, the notable structure of a uni-body vehicle and are the connection/attachment points for the front and rear ‘clips’.

You can drill into them if you like but again, they’re the car’s frame and you’ll be providing an additional pathway for corrosion … corrosion that, once present, can’t be repaired.

 

So the wiring is for my O2 sensors that i relocated behind the cat... ive been through here for hours trying to figure out how to relocate O2 sensors on a 99 cali spec but didnt find anything that was a clear answer to my problem. ( i replaced entire exhaust and only had somewhere to put the upstream sensors(in the cattman manifolds). The down stream o2 bungs were obviously removed with the stock y-pipe.

Long story short i had only half an idea of wtf i was doing the whole time and just went with it and figured id clean up at the end.

This was a major concern of mine thanks for the clear answer. I was definitely worried about cutting into the 23 year old under coating and creating potential for rust. Maybe ill get some heavy duty metal wire ties and make some sort of bracket to hook to the alignment holes.

 

Those are not the main structural rails. They are a semi-tubular underbody reinforcement. Yes you can drill a hole or two.

 

No offense, (I'm from Newark myself) but the car is 20+ years old and if the rails aren't rusted out by now a few little holes here and there aren't going to cause any more damage than he already has.