I know it's too late, but for the next project, sand all wind/flap surfaces with a 3 foot aluminum sanding bar with 320 or 220 grit paper. This will eliminate any high spots and reduce the chances of sanding through. At least this works for me. Good luck.
Don
Yes, knocking down those high areas is mandatory. You cannot do this afterwards once the covering material is in place. It's also important to really fill the wood grain before applying covering material, with one final scuffing of all wood areas.
Also, IMHO I feel it's necessary to apply dope to the rib edges and the cap strips. You can easily stay off the rib edges the first few coats of dope that's applied to the covering if you elect to.
Sanding the dope on open bays. I sand lightly with little pressure, just to scratch the dope up and you can stay off and away from rib edges with no difficulty.
And the "three' coats of dope?" You may need 4 or even 5 depending on your mix or if your covering material slackens and doesn't stay drum tight.
IMHO there should also be more conversations about the use of silk. I will never use anything except silk. I've been down the other road.
I find silk takes less dope to fill and with my CA method of applying silk dry you can cover a full wing in minutes ready for doping. Yes, there's stuff to know about this CA application, but once mastered I'll bet, "You'll love it, or list it."

BTW. I'm not the only one using this CA method.
Or, you can just use silk and apply it the "traditional way." I always iron the silk first.
Why do I pitch Silk? Try to tear silk. Good luck. Try to tear silkspan, polyspan, or covering "papers," a caveman could easily do it, even a child. Silkspan and similar papers will fight to be laid down at wing fillets or compound areas, silk will easily conform to compound shapes and fillets without having to make "split" cuts. I'm guessing here that this is done?
Silk, 5 yards only 15 bucks. Experiment a bit and I'll bet you'll fall in love with silk.
Last, primer. Best to not apply primer heavy in open bays. A heavy buildup of primer could crack or split in these areas. Wood areas you're good to go so knock yourself out. Most of the applied primer will be carefully sanded away. I sand the primer dry, vacuum, tack rag, clean carefully with a solvent then do my masking tape pull test. Ya gotta make sure all applied primer and paints stick as you progress. I do no wet sanding at all because I don't compete and I'm not pressed to finish, "front row quality."
Everything I've written above I've mention and I have many photos in my Build Threads showing this easy process.
Works for me every time.
CB