The pitfalls I can think of are that if you don't take it off at the gutter you leave the rust behind. Weld through primer wasn't used when these were made so they are all rusting at the overlaps. Take the guard off properly and refit with weld through primer. The other issue is welding the seam. Most people will stitch tacks with a mig but then its very difficult to metal finish due to different hardness of filler wire so you might end up with lots of bog, thin spots in the old metal when grinding the weld back and maybe not full peno leaving effectively a crack underneath that needs to be sealed. Tig might be ok though.
If you want to learn more about proper metal finishing methods check out this video
https://www.youtube.com/watch?v=IGElSHzm0q8 and buy his dvd. He explains really well why its better to oxy weld panels.
To pop the spots with heat I would use oxy to get a small puddle going. Maybe use a mill end weld drill to thin it down a touch first. But if you are careful with a mill end drill you can get them off without barely touching the metal underneath.
If you want it too look original you can always fill the holes and spot weld it back on.