Try hand bending to reshape
Without photos it is hard to access ... but assuming your frame is not damaged from shipping or welded incorrectly depending on how bad the fit is, you may be able to correct it yourself.
My canopy frame did not even come close to sitting flat on the canopy deck on either side with or without the 1/8? thick cardboard spacer in place. It sat flat until around the aft edge of the instrument panel then lifted on a steady angle so the aft end was quite a ways off the canopy deck ? at least 3/8" or so. Didn't measure it, but it was way off.
To resolve the issue, at the location the canopy frame began to lift away from the canopy deck, I lifted the canopy frame up and slid the plastic covered handle of a needle nose pliers under the frame ans slightly forward of that point ?. while pressing down firmly at the location where the handle of the pliers was under the canopy frame (to keep the frame firmly on the pliers), the square tubing was GENTLY flexed downward further aft to induce a slight bend beginning at the handle of the pliers ? go easy because the aluminum tubing is thin and bends easily, one does not want to over bend.
Went back and forth from side to side and worked my way aft. Think I ended up bending at three or four locations on each side. I took my time and within 15 minutes or so had the frame sitting perfectly flat on the 1/8? cardboard spacer. Also had to flex the aft bow a little aft as well ? then re-tweaked the frame a little more to perfect the fit because it moved a little while flexing the aft bow in position.
Hope this may be of help.
Happy Building,