Battery:
I would like a 6 or 8 cell LiIon battery, just because I like piece of mind and I will have more current draw to run the electronics than the average custom bike. An 8 cell is still light years lighter than an AGM or lead acid, so that's all good.
Fuel Pump:
As far as a fuel pump goes, regular inline auto fuel injection pumps pull WAY too much current for a bike, and they flow too much volume as well. Then you still need a pressure regulator and a return feed from that, and a filter, which the Honda unit has all built in to one (relatively) compact package. So its a simple low current draw solution, that happens to be pretty cheap too. You can get new ones for $100, and much less for a used one on ebay (I paid $47 shipped!).
Tuning:
For starters, I'll just be controlling fuel, no spark, so it simplifies the initial tuning procedures. I'm still debating narrow or wideband O2, but I've seen cheap wideband controllers like this that might change my mind:
http://www.ebay.com/itm/APSX-D1-Digital-Wideband-WBO-Controller-Enclosure-/181273702156?pt=Motors_Car_Truck_Parts_Accessories&vxp=mtr&hash=item2a34c12f0c
Tuning with the Microquirt is relatively simple with a laptop, but yes, lots of reading. You data log by going for a ride, then tweak, rinse, repeat. But the great thing is you can change parameters whenever you want, no dis-assembly required. And upgrades down the road like a GM LS1 style ignition is a relatively simple software tweak.
Rims & Tires:
I've got quite a bit of room for a tire in the front. I think I can fit a 4.60-17, but I will be measuring twice, ordering once (hopefully). I have some test tires on the rims to mock up. My original fender will be coming off for a custom solution, so all I have to clear are the fork tubes.