Hi David,
Congrats on your bike! I think the first order of business would be to look over all of the Whizzer stickies posted atop this section real good and make the appropriate modifications as required, of which there will be enough. Funny you mention you have a 2008 model; so do I, but it's the NER Whizzer with the CVT transmission and the block head motor. I haven't had her on the road as I have other projects on-line at the time.............but soon enough she will be rolling!
Besides getting intimate with the Whizzer Stickies on this site, another recommendation I can give would be to subscribe to the Whizzer Newsletter that is published monthly. Quenton Guenther writes up an informative column every month on the new model Whizzers and those columns alone are worth their weight in gold with the great technical information they provide.
As far as your questions go, again, the stickies above answer all of your questions, but for starters this is what I accomplished on my NER (with future mods pending): Removed head and sent off to Quenton, who milled the head for better cylinder sealing and a little more compression........factory mushroom lifters were removed and new Quenton mushroom lifters installed (the original mushroom lifters are simply not up to the task and will fail early in the motors life........new copper head gasket and modified cylinder head bolts installed........ You may expect at a minimum to have these mods done on your motor too. And then there is the crankcase vent system which is in need of a little work. Again, refer to the Quenton mod. He has spent a lot of time trying to engineer a system that prevents the oil from being blown out of the crankcase vent system and it seems he has found the cure for that one.
Wheels: I have read where a lot of NE5 guys went to an American made Worksman bicycle wheel which is a stronger wheel. Again, my NER, a different animal then your NE5, has a little bigger wheel to accomodate the 3 inch wide tires. Speaking of tires, the Schwalbe Fat Frank tires may be a good choice to consider. I believe they are German made and the reviews for them have been positive........
Clutch: Again, I refer you to the Whizzer Stickies. I know there were issues with bearings, so you want to do that research and go from there. Again, my NER has the CVT, a whole different design, so I am not familiar with the Whizzer Clutch system and it's idiosyncracies!
I think you are on the right track with your questions! It's a question of making the basic package dead-on reliable and bullet proof so it doesn't leave you stranded on the side of the road. Looking forward to reading of your progress!
Take Care,
Mike