Do not disconnect anything. You'll just create a bunch more codes.
Just go thru your Climate Control method and for each module, when it asks "PCM?", "TCS?", "IPC?" etc., it's asking you if you wish to drop down into the menu for that module. You say YES by pushing the Fan Speed UP button, and you say NO by pushing the Fan Speed DOWN button.
For example, if you have any PCM codes to clear, then when it asks "PCM?", say YES. Then it will ask "PCM CODES?", say NO (because you already know what they are). It may present other questions about the PCM, but keep saying NO until it asks "PCM CLEAR CODES?", say YES and it will clear all PCM codes.
Then you hit the OFF button to go back up one level in the Menu System. Tap the OFF button until you get back to "PCM?". Now say NO and it will move to the next module.
Side note: If you keep tapping OFF, it will back out all the way back to the Light-Test and start all over again... or tap OFF during the Light Test and you'll exit Diagnostic Mode altogether and be back at your normal dash-board.
You do this for each module, one at a time, to clear all codes. It's long-winded and cumbersome, but gets the job done.
You say to yourself, "Gee these codes are nice to know, but what a pain in the ass. I think I'll buy myself a little scan-tool." The price runs the whole price range from 20 dollars for a cheap reader-only, to several thousand bucks for what the Pros use. For 30 or 40 dollars, you can get one that will read all codes at once, and clear them all at once, and it will do it for most ANY car from 96-on. There's a connector to plug the scan-tool into, under the left side of the dash on the driver's side.