I'd first remove all of the flavorizer bars and light the grill as it sits. If you have very uneven heat, my guess is that you may need to clean up your burner tubes. The flames should be uniform across their length, if not you can remove the burner tubes and either replace them if they are rotted through, or wire brush to clean the holes and then try again without flavos on to see that you have even flames. You have to be meticulous, you want the holes in the burner tubes to really be perfect. A wire brush does wonders here, and you can even get more meticulous with a tiny screwdriver etc.
I wouldn't drill holes in the flavorizer bars, number one you now will have holes in them that will allow grease and grime to cake up the burner holes below, making your problem worse after a short while. Grease will fall through the holes and cake up the exact areas you are trying to open up. Second reason I'd advise against putting holes in the flavorizer bars is that where the holes are drilled, it's like giving rust a head start and you will go through many more sets of them than if you just use them intact.
If it were me, I'd focus on the burner tubes.
Good luck!