Should I try to use extra wax on the edges to make everything level?
Any input would be appreciated, thanks.
Don't exposed wax on the base. If you can scrape and are still getting wax off on a pass, keep scraping. Waxing is endless scraping.
Once you can't get any more wax off with the scraper take a nylon scotch bright pad (same thing you use in the sink) and buff the board a little. You'll get a slight fine powder. That's enough polish for a basic wax. There's more you can do if you are seeing really wet conditions or are anal. See the stickied tuning thread for more info.
Exposed wax will slow you down. Never leave exposed wax on your board. Only leave exposed wax on your buddies board and challenge him to a race with a 6-pack as the wager.
Now to the warp. Did you have the bindings on the board? Bindings will pull up on the board warping the base slightly. You'll only notice it when scraping. I can't comment on whether it was designed in there or not.