You need to do it all. Port, crank, domes, pipes, jets.
It's really a package that you need to complete to benefit from the whole thing.
It's gonna cost you since you have no useable parts.
You can run the stock parts, but don't expect any difference after all the work is done. The builder will recommend pipes port work carbs (jetting for stock) to you. Then it goes to the clutch, and trans. I wouldn't run an oem basket in a stock bike. So a basket, new clutch is usually a good idea. All worn out shift parts. If you would like the bike to shift better you can cut the trans.
All seals, new cables, and other odds and ends your going to find as you tear the bike down.
It adds up fast.
But don't be discouraged. You can get a stock crank trued and welded and get it ported. Save you a few bucks. Read up there's plenty if options. And used parts is a huge money saver.
Regardless, any ported motor stock or stroked is leaps and bounds over stock.