Mine was pretty rusty when replaced as well..I added some reinforcing metal underneath the bottom where mine had rotted away..
I'm not sure where your "bump" is, but the windshield glass needs a nice consistent surface to rest on... It can't be really high in one spot. That's probably the most critical aspect of it. I'd try to remove and/or deform it so that you get a nice mounting surface for the new panel. Test fit the glass after tack welding the panel.
The cowl will not really sit on the new upper dash panel, and the fenders should get only close to it in the uppermost corners.. Beware that the corners of the fenders may hit that panel, so if you're too high near the fenders, you may need to reshape some metal a bit.. Test fit your fenders after you tack weld the new panel in.
When you've completed, seal the new panel completely in order to eliminate a re-rust.
Fenders aren't hard to take off.. just a bunch of potentially rusty bolts... I've had no problem realigning them, but some folks say thy've had to jack the nose of the car a bit before attaching fenders...
