So I finished putting higher jets in my holley and I stripped the threads in the main body where the bolt that holds the float bowl and metering plate in, this caused the bolts not go all the way in and tighten causing it to leak really badly. So my question is how can I get these bolts to sit in there correctly.

You can try cleaning the threads out with a tap of the same size thread. Those aluminum castings strip very easily or pieces of aluminum gall up the threads. I rebuilt my carb on Friday and almost stripped out one of the holes.

Just be sure to use a "bottoming" tap. You may end up needing a heli-coil kit

czc,
Holley makes a helicoil kit for those bolts. It is 1/4"x28 or maybe 24, dont remember for sure, but not a popular size thread. I have the kit and probably fix 20 of those holes for guys each year. Not a hard job, you dont really even need to drill, just use the helicoil tap with a lot of pressure, and thread cutting lube and it cuts fine.

Are they not a #12-24 thread? Helicoils do a good job on these. Worked for me.