I don't know the best way, but I can tell my experience with cleaning the upper intake and throttle body. I had to take the upper intake off for some other work that needed to be done. I decided that would be a good time to clean them. I used carburetor cleaner and TB cleaner in aerosol form. I got a lot of crap out of them. There was no damage to the plastic. I turned them every way to get any residue out and let sit in the sun for about an hour to make sure everything was evaporated out. I didn't have an air compressor with me to blow it out.
I put everything back together and went to start it. It would try to start but would not continue running. Each time I tried it would get worse to the point that it would not fire at all. Once it even backfired through the intake. I eventually gave up and let it sit overnight. I tried it in the morning again and had no success. Through the day, I decided I would just have to tow it to the dealer and let them figure out what was wrong. When I got home that night I decided to try to start it again before I taking it to the dealer. It fired right up like there was never a problem and has been working well for about 2 years now.
My only guess as to what happened is; some of the cleaner must have gotten trapped in the intake and was causing an error in the readings at the O2 sensor. After sitting long enough the cleaner eventually dissipated and no longer created a problem. I would have second thoughts about cleaning it that way again but if I did I would be sure to have a good air compressor to blow the intake and TB free of cleaner.
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