problem passages

Depends on why it feels wrong. With my novel, some stuff didn't work where it was so I put those bits into a separate document and carried on writing without them. I then looked over them when I'd finished that section. Most of them ended up slotting in to other places perfectly. (Well, I think they fit in perfectly - have yet to get it published so no outside proof as of yet!) If it just won't scan/flow/whatever, ask someone else to look over it as they may see a flaw you missed.

I've always found it's best (never, ever scrap!) to shove it away, out of sight (and mind) for a few days and then review. It's easier, with a fresh mind, to see the flaws that way.

Stick them all together in a separate file. Then, when your feeling either brave or desperate enough, send the whole bloody lot to a publisher. It probably won't get published but it'll give you a laugh to imagine they're even considering it.

eat more fibre

Like Andrea says, never ever scrap, especially if you write on a computer. I've been through several [re-]drafts of my manuscripts and what I do most often is to use a copy and give it a version number, to distinguish consecutive version, for instance my novel Peccadillo started of as Artisan 1.1, with redrafts 1.2, 1.3, 1.4. Then I realised an entire storyline didn't work, so I started at version 1.5, but opted to give it another title, Peccadillo, and number 1.1. This went to redrafts 1.2, 1.3, 1.4, and [when I started to scrap a lot of words] 2.1. The current version is 2.2 [the slimmer revised version]. Anyway, I never throw something out. Sure, it means you are using memory, but even the fattest version of Peccadillo was only 998 kilobyte, so you can fit quite a lot of mss on a regular harddisk. Hope this helps.