A few years back I bought a GM cowl induction hood and I just couldn't get it mostly to fit the contour of the cowl panel especially on the driver's side, but also the surrounding metal at the front corners and front center peak.
Finally I got frustrated enough with playing around with the latch, bumpers, and hinges, and placed it on my wood patio deck with towels under it in specific places as to not dent or crimp it and even more towels below and on top of the areas where I thought it need a little tweaking and went for it.
After an afternoon of careful pushing and bumping (usually with the flats of my hands) it came out even, level, and now fits perfect...
Just take your time and don't try to do too much all at once. Keep checking it as you go even if it means multiple installs back on the car - which is really the only true measure of success and progress - and especially again, keep it all well padded.