1. Getting cold while sleeping: two questions back: What sleeping pad were you using, and what clothes were you wearing? Both will have an impact on keeping you warm, in addition to your bag.

It got about 5 degrees colder than your bag is rated, and Marmot bags tend to run pretty true to the rating - so it's reasonable to expect that you'd feel a bit chilly, probably from around2 to 6 a.m. or so.

However, if the chill seemed to be seeping up from below, rather than coming in around the bag, the culprit might be your sleeping pad. Each pad has a different R-value; MSR actually advertises their R-value; other pads will give a temperature rating. If it gets colder than the pad is rated, you'll feel cold seeping up. (That happened to me once with a BA Insulated Air Core pad, rated to about 20 degrees. It dropped to about 12, and sure enough, around 4 a.m., I could feel the cold underneath me.) The only good solution is usually to add a closed-cell foam pad under the regular pad, though I've also had some luck using one of those heavy duty "survival" style space blankets, with the shiny side facing up, as a ground cloth under my pad.

Finally, if you're going to push the limits of your bag and pad, you need to sleep in some warm clothes. I usually sleep in my long john top and bottom, and add a stocking cap, balaclava, liner gloves, and extra socks as needed. When I'm really trying to push it, I'll sleep in everything I've got - on the aforementioned 12 degree night, I slept in down pants, down hooded jacket, down mittens, and down booties over the long johns and balaclava, but I was using a 30-degree bag so I needed the extra insulation.

2. Clothing: for a 2-night trip, I'd have the same list as you, except no spare shirt and I'd add a down sweater-weight jacket (or fleece jacket.) I'd be wearing the shorts and shirt, and maybe the long underwear top and bottom if it was in the forties; I'd wear hats and gloves as necessary. The down/fleece would stay in my pack, and I'd have a spare pair of socks. I'd also bring a light windbreaker (Marmot Ion, Patagonia Houdini, or similar) which I'd wear as needed. My rain suit would provide me with a backup wind layer, some extra warmth, and my rain pants would work as long pants. For six days, I'd add another pair of socks and consider a change of shorts (or underwear) and that spare shirt.

3. The only good way I've found to deal with long, soaking rain is to get out of it as soon as possible: head back to the car, pitch a tent and wait it out, etc. No matter how good your rain gear is, if you walk in an all-day heavy rain, you'll end up wet.

As far as getting a stove running in the rain, I tend to find a drier spot (undercut shelter in a ledge, or maybe I'll pitch my tent fly only to make a snug little lunch shelter), and then start the stove as usual. If all else fails, I will very, very carefully cook in the tent vestibule, being very careful not to let the stove flare or let the stove or a hot pot get too close to the rain fly (which can melt if heated.)

I'll never cook inside the tent, not ever, period. If it's raining hard at supper time, I'll consider eating tomorrow's lunch for supper, and stopping to cook today's supper for lunch tomorrow; then I don't have to light a stove at all, since I eat a cold lunch.

If I were knowlingly going out on a trip where it was going to rain for several days, especially with a group, I'd probably pack along an 8x10 or 10x10 silnylon tarp, and pitch it as a separate cooking fly. It also makes a nice place to sit with other hikers to pass the time.