I admit those are the only ones I've had the chance of testing on Swain but they work pretty good. Magic penetration should be self-explanatory; mana regen seals help when an overzealous lane partner makes last hitting hard for you, and they make a difference late game as well; MR/level glyphs help you survive against champs like Kassadin and Veigar until you get your Banshee's Veil; HP quints for the same reason. That said, feel free to experiment. If I had every rune bought I'd probably switch my glyphs to AP (probably flat ones) but that's about it. Just don't use CDR runes if you have them, since this build finished already gives you 40% CDR (hell, even more with the masteries).

I'm not a fan of Doran's items, but if you don't feel secure without that additional HP/AP/mana regen, then by all means. I'd rather have my boots. Swain has a pretty short range and getting in and out of it quickly helps. The potions also help you last until level 6, when health shouldn't be such a problem anymore with your ultimate.