for the side you've done already id just tap down that large high spot in the middle and then put a filthy big skim of bog over the entire panel - front to back and top to bottom. might take you all day to rub but it should improve what you've got there.

for the other side id go get some bonnets or boot lids from the local panel shop or scarp yard and cut out your fill sections an inch wider than the hole. once cut, try and put some curve in the sections to suit the natural roll of the canopy panel. go to the hardware and get some sika or to the auto shop and get panel glue. glue them onto the inside and then put a spot weld every inch or so. then bog the entire canopy panel. tapping down highs and trying to push up the lows as much as possible (less bog)

NOTE: ive never done this before but its how i would IF i was going to fill them myself (ie not employ a welding contractor)

best of luck!