My original plan was to rebuild my motor. When I got into it, I found a lot wrong and no longer usable. This led me to buy aftermarket pistons and connecting rods.

I'm having a problem with the connecting rod bolts hitting the girdle due to the bolt heads being too tall. My guy at the machine shop said I cannot shave them or it will ruin the strength of them. They are Skunk 2 connecting rods from ProCivic.com with ARP bolts.

Does anyone know if there are different bolts I could use?

 

Your machinist is lying to you. You can machine the girdle for rod bolt clearance.
We just did this on my son's d series engine to clear his eagle rods with arp bolts.
There's also a you tube video showing it done.
Basically you mock up the bottom end, and mark out where the bolts will hit, then it's just a matter of machining a 3/4" slot for clearance of the rods and bolts.
When you look at the girdle from the cranks side, you'll see that it tapers in the center. That's your start point, drop the cutter .250, and you machine outwards.
For the side/spot will the oil passage, you can easily take .080 off it without any trouble (won't get into the oil passage. We actually went .100 on that part, as it still looked close. The guy in the video only went .060 there.
I hope this helps.