I still think you are in for a world of hurt with that plan, but if that is what you find enjoyable then go for it.
As for your question, you'll keep most types of mutations while you are transformed. If you naturally have claws and use statue form, your statue form will claw things instead of pummeling them. In regards to the poison resistance thing, there is only one level of poison resistance. Once you are resistant, you are resistant, so stacking wouldn't come into play there. Resistances that have multiple levels can stack fine with a form though, so long as resistance doesn't come from a piece of equipment which gets melded away for that particular form.
Spider form still works fine with Chei. The thing is, trolls of Chei will never get his full stat bonuses, so I'm not entirely sure they're compatible.
I actually prefer Sif Muna to Vehumet most of the time. The spells granted are generally better after a short while, and the channeling is great (especially for kiting ).
Yeah, Trolls wouldn't be a good Chei choice. Something like a sludge elf or a merfolk transmuter would be fine with chei though.
Sif used to be the better choice, but ever since the 0.6 Vehumet buffs I've always found Vehumet to be superior. Cheaper conjurations, longer range conjurations, mana for kills, and god-supported conjurations all combine to make a package that really outshines Sif now. These are bonuses which are always useful throughout the entirety of the game. Sure, Sif may eventually gift you all spellbooks, but usually you will end up finding all of the important spells as it is. Instead of random books, Vehumet gives you the books you need to kill stuff RIGHT NOW. You'll usually be holding all of Vehumet's books by the time lair is done. I am usually thrilled to get that book of power in my hands somewhere mid-lair so that I can burn mystic blast into my brain.
The only spells of consequence that tend to be hard to find are necromutation and controlled blink. Neither one is necessary for a low rune (or even high rune) win though, and even then you'll usually end up finding both of them somewhere.
The main reason to take Sif now is the channeling, especially if you can do it hungerlessly. Sif's channeling beats out the staff version pretty handily. So you might want to go Sif if you are a mummy and don't have hunger to begin with, or you want to guarantee yourself a necronomicon and channel in lich form. If you are playing a conjurer and aren't planning on abusing channeling somehow, I wouldn't suggest going with Sif.