"Are those closed cell torso length pads actually comfortable?"
Comfortable? I would say no but you can probably get used to using them if you are tired enough or just get used to it...kinda depends on what kind of a sleeper you are. I find a NeoAir WAY more comfortable than my closed cell RidgeRest...and the weight isn't much different.
"If I found a shirt I could wear while hiking in warmer temps but also sleep in as a base layer, I could drop the MH Carson shirt AND the Capilene 2 top. Anyone have any ideas? Maybe a Capilene 1 short sleeve?"
Hmm....I like to have as light of a baselayer as possible to wear while hiking. With a light shirt, you can always go warmer by adding layers, but normally I don't need anything more. I have a Sierra Designs baselayer T-shirt and a Patagonia one (Capilene 2 T-Shirt I think). Both weigh about 4.5oz. I like to have a spare because otherwise I'd spend the entire trip in the same shirt and I like to wash it occasionally OR if it's wet from sweat or rain then I have another dry baselayer tee for sleeping in. I probably shouldn't take two of the exact same thing though. I could take one baselayer tee and one longsleeve baselayer that is slightly thicker and weighs about 5.5oz. That would give me more laying options and be useful on colder days.
"The pants are too heavy, but I do like having convertible pants."
Understandable....convertible pants would be ideal. Perhaps really light ones exist, but I'm not aware of any really light ones. If you can't find any, you would be better off to buy the 4oz pants I suggested and some light shorts like the GoLite Baja's (3 oz) instead of your 17.5oz convertible pants.
BTW, supposedly the BPL Thorofare pants have a pretty good DWR on them which means they can function as rain pants too in non-extreme conditions. I noticed you don't have any rain bottoms listed, so these would actually add functionality in addition to the weight they save.
"The toboggan is a beanie. I've been trying to decide if I really need a balaclava with the quilt or could get by with a beanie."
I would get an insulated jkt with hood. The Montbell U.L. Down Inner Parka is really light (my medium weighs 8.5oz). Having your head gear connected to the jkt keeps you warmer....plus the hood can be cinched tightly around your face so it's just as good as a balaclava. Another advantage is simplicity. You're not going to lose the hood off your jkt or have a hard time finding it at dusk. Your pullover + wool hat weighs 16.2oz. An Montbell U.L. Down Inner Parka would probably weigh 10oz in XL and it would be warmer and simpler....but it does cost $165 unless you can find one in the gear swap.
"Dropping the headlamp would be an adjustment for me, but I think I could do it."
I'm a headlamp fan....they're just so darn handy in the evening. A handheld light works, but when you are sorting through your pack looking for something it's nice to have both hands free. Same goes for cooking after dark. The Zipka is a pretty darn light headlamp.
While I'm on the topic, what's up with AAA batteries in light weight headlamps? A high end AA lithium battery (ie. Energizer Photo Lithium) weighs 14.5g and can hold 2900mAh of power. That works out to 200mAh per gram.
The top AAA batteries weigh 7.6g and but hold only 1250mAh, which is just 165mAh per gram...nearly 20% worse. So if you have a device that needs two AAA batteries, you're carrying 15.2g worth of batteries which contain a total of 2500mAh of power. You'd be better off with a single AA which is 0.7g lighter and has an extra 400mAh of power. I would love to see a version of the Zipka with fewer LEDs, the same great strap, but a smaller body that just holds a single AA.