I ran for a few thousand miles with just an after-market muffler.... nothing else done. I was worried (like you), but I didn't let it slow me down!
It ran good, but my after-market can flows a lot of exhaust out of it's 2 1/12 inch outlet.... I suspected that I needed a little more back-pressure. I was able to perform a little modification and was pleased with the result.
Cutting to the chase, I wouldn't worry. I changed my spark plugs out and they looked PERFECT after having run the after-market muffler and no other modifications.
Then I ordered the TFI, K&N, and cut a hole in my air box lid in preperation for the Stage 1 mod'. But it didn't arrive in time for my weekend ride. So I put the dirty factory filter back in the bike, replaced the snorkel, and stuck the air box lid (with it's new 1 1/2 inch hole cut into it) back onto the bike. Between that factory air filter, the hole cut in the lid, and my after-market muffler in place.... by bike ran TITS!
So I wouldn't worry about it....
-- BUT --
when I stuck the TFI in, set it with the settings Holeshot gave me, and replaced the factory air filter with a K&N, my bike ran smoooooth!
Don't worry, then someday kick down the bucks and get the Stage 1 set up from Dale Walker of Holeshot~!