i would do like 1 inch weld 1 inch gap all the way down when you weld it in so it wont twist the body as much as it would fully welded, then glass over top that and there ya go.
weld that shit. i had mine done with metal2metal, and it cracked. so now i have to grind it all out and redo it right. and yeah, i;'d fully weld it. just go slow. i got a pic of my fender welded up in my profile.