If I don't remove the air pump and leave it functional for now.. should I still grind the little tubes the come through in the header pipes? they stick through about 1/4" or a bit less. would this effect anything that could cause backfire through or anything? I was told I should leave the sytsem intact for now as they are suppose to start doing spot checks on the road. just figured since I had it all off right now to fix the engine but I better leave it for now. so only quesiton is about grinding the little tubes flush.

thanks

Yeah, grinding out any obstructions or stray welding in the entrance to the header primaries will help.

thanks.. I just didn't know if it would cause exhaust to flow back to the air tubes.

If you leave the AIr pump on without anything connected to it it will sieze up. I have had this happen to every 3rd gen that I have removed the AIR from and left the pump behind. Take it off if you can.

I 'm going to leave it functional. I just wanted to know if grinding the nipples the come through the headers flush will cause any adverse effect like combustion blowing up inside the tubes to the air pump

You will be fine.