Would there be any issues if I drilled a couple of holes in my lowering link clevis to lower it 1/2"?
I cant answer that question, but i took a lowered 2011 XR out for a spin in Arizona for a few nights and scraped the exhaust pulling out of a parking lot... I'm not sure if anyone else had that problem but, food for thought I guess.
Yes you can lower bike by drilling hole. You will have to readjust your belt that will be a must. You will have to run more air in shock.
Yes just about all baggers will scrap pipes if you pull out to fast.