I've done this with two 2-stroke mopeds and both ended up great. I used vinegar for both, and I had to let it sit for a week.
After I drained the vinegar, I washed it very good with soapy water, shook them out the best I could, sprayed a bunch of WD-40 and Fogging oil in there (which probably did nothing), and then immediately filled it to the top with mixed gas and never had any problems. I think the oil in the gas helped out a ton, but, looks like you already added straight oil.
Maybe it's because you used a really strong acid? I chose vinegar because it was way less strong than The Works. It takes way longer, but the result I got was still awesome, even though it took a week.