I'm no glass expert, but I can tell you what I did, with advice and help from the local canard guru.
I had the same situation you describe with the spinner low. Mine was about 3/8" and slightly offset to one side. I considered adding washers to the engine mount, but I was very happy after about 180 hours with the speed and handling of the airplane, and was reluctant to change the thrustline.
All of the glass airplane guys who looked at it were unanimous: Cut the offending part off. I considered making two cuts as suggested above, but they just snickered and said it was less trouble to just make a new piece.
With direction and encouragement, I used a pencil to carefully trace around the spinner. Then I removed the top cowl and used one of those little air-powered reciprocating saws and cut the hump off entirely, leaving only the ring behind the spinner, and a little flange on the back side to maintain its shape. Using a cardboard dam taped under and around the hole, I poured some two-part foam in and let it cure (10 minutes maybe) and pulled the cardboard off before finishing trimming the flange off the ring.
20 minutes of trimming with files, rasps and sandpaper had the shape I wanted. I did have to trim a lot of foam out from the back to clear the ring gear and trin the center front baffle.
Then I sanded a few inches out on the cowl, masked the foam very carefully with duct tape and laid up three layers of heavy "biaxial" glass and EZ-poxy (because it's what one of the EZ guys had lying around). Turned everyting over, tore out the foam, and made another layup on the inside to pretty up the edges.
Finally put finish paint on it a couple of weeks ago
This sounds like more work than it really was. Definitely less than starting over with a new cowl. Hope this helps some.