Those wheels look OK. Personally I prefer a hand built spoked wheel for its strength to weight ratio. They look like they'll be fine. The disk brake mount for the sprocket is a great way to go. Why such a large rear sprocket? Do you have some steep hills around you? The normally recommended sprocket with the EZMotorbike kit is a 56t. The 62t is a good climbing gear but will limit your top speed a little. I also like the Planet Bike fenders.
As for tools, you don't need any special tools for removing the one piece crank. A large adjustable wrench, an old screwdriver, and a hammer are all you need. You might need special tools for installing the three piece crank depending on the style of the bearings. If it has loose or non-cartridge bearings you can probably get by with the same tools as above but there are bicycle specific tools that do a better job. If you are installing a crank with cartridge bearings, you need a splined bottom bracket tool. I'd also recommend a torque wrench. With the three piece crank it's important to get the right torque for the bolts that attach the arms to the spindle. If you ever need to remove the crank arms you'll also need a crank arm puller.
For the freewheel, you need a special freewheel remover tool . There are several types of freewheel removers. You have to get the one that fits into your specific freewheel. Once removed, you don't need any tools to install the freewheel onto the new wheel; you just screw it on. It has right hand threads which tighten when you pedal.
