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Since you're not too new to rooting and ROMming, I won't go into too great of detail. Make a backup of your stock, rooted ROM. If you want to go back to stock after flashing a custom ROM, just go into recovery and flash the backup of your stock ROM. Easy peasy. Or, you could just flash an SBF file and it will take you back to out-of-the-box software. You'll just have to re-root. I'm not sure about having to re-unlock it.
Sent from my 3rd reincarnation of the ever-so-lovable Droid
If you do it with the stock system, yes (either in settings or in stock recovery). If you do it with a custom ROM, then you'll likely do it with a custom recovery like clockwork, which does not wipe the internal memory. Also, unlocking the bootloader wipes all memory, and running those files linked above to return to stock will wipe all memory.