Well if you had a backup of the stock ROM you could restore to that and then do a factory reset.
Otherwise, the important thing is to wipe before flashing the ROM, not after - you'll get in a terrible mess otherwise.
I don't use ROM manager myself - prefer to boot into recovery and do everything from there ("full wipe/factory reset", and I'd probably wipe dalvik cache while I was there - that option may be under "advanced" - then flash the ROM). But I expect ROM manager's wipe does the same thing.
Read the first post on that thread. It explains what options are available: you can have it completely stock, except rooted, or else stock with a range of options. If you select the version with init.d support you can add most of the options later - some of them aren't supported on the base version of the ROM. The init.d support doesn't otherwise make much difference, so if you don't want the options you can still use that version (which doesn't change the radio as part of the flash - if you prefer to avoid unnecessary radio flashes, that's probably a bonus).
This is the ROM which I used to use before DeFrost, though I progressively added more and more mods to it, and I always found it to be very solid. And as the post explains, if you want it totally stock (even the "not so quietly brilliant" boot sound) even that's possible as well.
