17" wheel swap from new gen or 300 is doable. There is a sticky how to thread on it. Down side of them is they are still expensive because people with r3's are snagging them and converting them because ifc the lack of extra r3 wheels.
I went with ex 500 wheels. They are very cheap by comparison. They are about 1or 2 lbs heavier than new gen wheels. Buy lighter tires to make up that difference if weight is a concern.
Front end, well your wallet is the limit. Still have hold valve emulators. Rigor intinmidators for slightly more than the gve. Intinmidators are install and go, no tuning like gve. But the 2 bikes I have rode that have them, no tuning nessecarry.
There is a guy on east coast that will install gsxr internals into your pregen forks. I believe it was about 400 bucks for that when I spoke with him.
He also sells matris f15 cartridges that drop right in after he changes the shim stack. It was north of 600 for them. But damn they are nice. Easy peasy adjustability. I still running stick clip ons with them. Remove clip on to gain access to adjust the front end.
Also added bonus with them is I can remove them and use them in New gen 250 or a 300. Internally all 3 have same diameter fork tubes.
Gsxr shock is the cheapest way for adjustable rear.
Pods belong on your cb650 bobber project. Can you make them work, yes. Will they perform as well as stock air box? No.
Exhaust, used muzzy is the way to go if you can find it. I see there was a post about how to make a 2-1 for pregen. Do a search and you will find the how to slow your already slow bike down some more with homemade exhaust.
cheers