My thoughts as I'm currently in that weird space between printing well autonomously and some irritating glitches from time to time.
I thought the same way you did and got some nice upgrades for my mendel out of the gate when i started, for example; I started with the LMU88 linear bearings, and a heated bed. I really recommend starting with these.
I guarantee that you'll find something to tweak and want to rebuild your machine no matter what you start out with. Its a very hacker project, most of the "fun" is getting it to work exactly the way you want it too. For example, i wired up my own electronics with an lpc1769 on a breadboard (kinda like the Smoothie on a breadboard project) and hacked some source code from another project for my own custom G-codes. (G-code to do a "lights - out" and some watch dog internal programming). Fun stuff.
If hacking isn't your thing, I'd recommend getting a complete kit and follow it exactly and throw away all thoughts of improving it.
Extruder Fan cooling mount isn't too necessary from what I can see.
Material holder doesn't require tearing up the machine to mount. Some implementations of this are better than others IMO. I'd hold off on this one untill you see one you like.
SD card reader you can buy at microcenter for 5 bucks, get a microSD card with full sized adapter. just lookup the pinout for SPI mode SD cards and solder to your board's apropriate SPI port. Worked for me.
Z mount adjusters would be great for my setup. Haven't figured out how to get this to work right yet... leveling the board is a pain.
Endstops, i've had good luck from radio shack roller switches, though, I hacked the source code to make 'em work the way I thought they should work... I only implemented the home endstops. The current source avaliable for my board doesn't generate an appropriate interupt if it overuns any of the axis's.... but then again, printer interface will show you if you are running over your axis's anyway.
That's my two cents. Hope it helps. I think i might try a test to see if a screw drive on x and y is feasable or just ridiculous. The X axis belt drive is making me crazy today...