Well, since I'm working on the same kit at the moment I'll jump in with my comments. However, you should know that I am *NOT* a "ship modeler" - I tend to build all sorts of subjects - so I don't have answers to many technique questions.
Anyway, here's my comments on the YMW kit (nb: this is my first resin ship model, so perhaps ALL such kits suffer these issues and my complaints are unwarranted). I agree with every one of your observations. When I first unpacked this baby, I was very excited about it. Now after having become intimate with it, I'm frankly quite disappointed, especially given the premium price being charged. First off, the hull (I prefer full-hull models). My top/bottom halves were at least 1/2" off in the length dimension, and probably closer to an inch: unacceptable, even with the given "shrinkage differential" explanation. I had to do some serious cutting/shaving/reshaping on the lower stern section to make things match up. Next up is the forward superstructure: nothing fits correctly. As you stack the decks up, you'll see that the aft end (basically the lower section of the forward funnel) is "off" on each level, again requiring significant "bodywork." In the 03/04/05 levels, you're going to find surface irregularities in the deckhouses that are probably a scale foot deep. No problem - just fix 'em, right? Sure, but this means scrapping ALL the factory surface detail.... why did I spend all this money on this kit again? Be sure you check the squareness of the structures: on my example the stacked-up forward superstructure was nearly a tenth of an inch taller at the aft end than the forward end. Again, unacceptable.
Jumping to the cast metal parts: so far the only pieces I've found in the kit which are salvagable are the main gun directors. The barrels are laughable: I contacted Burkhardt Masch in Germany who made me a set of turned brass barrels for both the mains and the 5/54s. The 40mm mounts are, compared to aftermarket, not up to snuff. Even the searchlights are not much more than little blobs of metal. Perhaps that's where I'm doing a disservice to Yankee Modelworks: comparing "stock" kit parts to aftermarket parts -- perhaps my expectations were too high.
So the way I'm looking at this project is this: the YMW kit is providing me with a (albeit expensive) jumping off point. The majority of kit parts are either unusable or require significant rework to bring them up to acceptable standard. I feel like I spent hundreds of dollars for a hull (and the hull needed to be fixed before IT was usable).
Ok, now that my rant is over, here's how I've been working on the kit. I put the hull together and got that all sorted, then started on the forward superstructure. Use cyanoacrylate (my fav is the ZAP in pink bottle: squeeze a puddle onto work surface and apply with small brass wire). I've been using Bondo Glazing and Spot putty for filling gaps since it sands easier than the resin: if you use anything harder than you're likely to sand more resin than filler. One issue I've run in to is I didn't really have a "plan" for how to configure this ship from the start, so I've sort of been flying by the seat of my pants on modifications. Which means, unless you sit down and do ALL your research / planning first, you're better off leaving the paint for when the major subassemblies are done. I use Mr. Surfacer 1000 primer with Mr. Color self-leveling thinner. A thin coat will cover your bodywork and show you all the areas that need additional cleanup.
Finally, don't get me wrong - I'm having a great time building this ship, and this forum is quite helpful. I guess my main gripe is that I expected more from the base kit than it delivered. The only way I'll know whether this is a valid gripe is to build another kit from a different manufacturer, and something tells me when my Montana is complete, I'll be wanting to build something different. Like a tank. Or a car
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FAQ
I am impressed! 
CA glue makes a strong bond between the parts, thus you have to assembly the parts quickly. But you can use two component glue which dries slower. One of my friends uses Pattex two component glue and he is very satisfied with it. 