IMO there isn't any reason to do a big bore unless you are going to do a port and polish, and possibly bigger valves. That's my two cents though. You could go to a higher compression piston instead of the big bore, and do everything else, and save yourself a few hundred. A port and polish is pretty reasonable depending on who you have do it. Some guys charge a lot, others dont, but as the old saying goes, you get what you pay for. The airbox lid isn't required, as long as you do regular maintenance on your air filter. If you go with the HC3, you should think about buying a better battery as well, to help turn it over easier. You could talk to Eric at EHS for a port job, Velociraptor, or DL. They have all done them on the XX. If you do this build, you should spend some money on getting it Dyno'd as well.
2008 700xx; Power Bomb header with power core 4 exhaust, Power Programmer III, pro armor nerfs, prm products control front and rear bumpers and full skid, 10" ITP rears, ITP Baja's fronts, RZR 2's all the way around, Uni filter, 13t sprocket, CCP steering Damper, DS450 shock swap, Dual Gasser Throttle, bar risers and Moose barkBusters. 730XX kit plus other engine mods!