Stock e-clips aren't too bad, but nuts are easier. Use the clear Scotch tape method over the e-clips during removal/install with an X-Acto knife to remove and small flat blade screwdriver to install them. Sure the nuts prolly weigh more, but it's not enough to adversely affect handling or acceleration. Too light weight is not good either. Do yourself a favor and buy the parts bag with extra E-clips in it...you'll never lose one that way.
Wheel bearings make a huge difference and if you're going to run Li-Po you definitely need them. Bushings won't last long at those speeds and handling will not be as good.