Hi benn600 - here are some food for thought on your various Q's and observations (in no particular order)
RC & K'Board: My HTPC Build includes the MS MCE IR Keyboard & Remote which MC12 supports out of the box. I use the Keyboard only when needed (eg config for Vista, MC12 etc). I've programed the IR codes into my Yami Universal RC so the one remote controls all my AV devices without mucking around with any third party SW. Nice and Easy but you need to make a registry change to turn "debouce off" (also in XP you need to add a patch to support the IR reviever). Result is that it mostly behaves like any other AV device
MC12 Startup: I boot straight into T'View (Blue Too skin), just added MC12 to the startup group.
Network: I can play media from both Local and Network shares over 100BT network just fine - max utilisation so far is 25% on my HDV files (not surprising as these files are encoded at 25mbs). I will upgrade my switch at some point to G'Bit but as I don't have any probs at the moment it is just not a priority.
Encoding: I also am uninterested in keeping compressed or transcoded Audio and Video and use original CD/DVD to create lossless rips for everthing that I want to keep in the library. For me I store all music as lossless WMA, and all Video in its original format (HDV, DV, MPEG etc) without transcoding (disk is cheap!). I however rip, store and manage my Music DVD's by tracks just like you do with CD's for me it is in the format of "Music Video\Artist\Album\00 - Title.MPG" (letting you then have playlists that mix and match Audio and Music Video tracks etc - very cool). I also use the same method to store Series based DVD's by Episode (eg "TV Series\Series Name\S01E01-Title.MPG) . I tend not to store my DVD's but when I do I use the same software to pull out the main movie and prefered audio track as "Movies\Title.mpg (note: none of this re-encodes anything - it is all bit perfect but stores them as individual MPG files NOT all collection of VOBS in the VIDEO_TS folder).
Storage: I was keeping two full copies of my media on both the HTPC and my main PC each with their own MC12 instance. Given my now limited HTPC drive storage (and recent network testing) what I really want to do is add a NAS via gigabit that I can keep in the back shed that holds a full copy of my media in case the house burns down or we get cleaned completly out. The HTPC would then just play the files over the network from either my main PC or the NAS.
TV/PVR Features: This has come a long way in the last year with basic support up and going but is still behind the competition in the more advanced features. So far you can watch, pause, and manually record a TV stream (will be added as a file to your video directory) from within T'View. You can also schedule a recording (eg by CH, Date, Time, Duration) but only from STD View. At this stage there is no EPG integration, control of third party TV equipment (eg sat box), CH mapping to #'s, or the ability to record and pause at the same time.
Dirt Cheap HTPC Build?: Everyones Idea of dirt cheap is different and will depend on how you plan to push Video/Audio out to your AV Equipment (I hate to say it but there is no point having a top quality collection being degraded by poor HW/SW). I've played with more combos than I care to admit trying to get to Quality Niverna on this and while I'm not their yet, I've been impressed with the performace of of my latest setup and in particular Intel's integrated X3100 graphics so far (compared to nVidia anyway). You certainly don't need a Quad Core but in my testing I can get one core up over 50% but the others are idiling along. I've also found the the Video Quality in Vista with Aero on is better than XP (no idea why) so you are going to want 2gb though I was just getting away with 1gb before. So most modern components will be fine but watch out for noisy fans and components (like an external LG burner that sounded like it was going into orbit when playing DVDs).
Thanks
Nathan