I pretty much never remove the choke housings. The passages in them are quite large and don't plug up. You can remove the choke plunger from the housing if you like. Then you can clean out it's hole, clean the plunger, and inspect it's rubber sealing tip. Maybe I've been lucky but I've never found a bad one.
For jets, all I will recommend is that you get genuine Mikuni ones. Shop around on the web and find your best price. I think retail is about $4 per jet but many places charge more than that. Be sure you get the correct type pilot jets. Two types were used in the 650 carbs over the years, the BS30/96 and the VM22/210. They look very similar and will physically interchange, but you must use the type your particular carb set was designed to use. In the case of your '76-'77 carb set, that is the VM22/210 type pilot. You can tell the 2 apart by which end of the jet has the metering orifice .....
You may have noticed your original pilots have no air bleed holes down the sides. You won't be finding replacements like that but that's OK. The standard style with the bleed holes work just fine. Apparently, Yamaha contracted with Mikuni to have these no-bleed-hole jets made special for them while they were producing the bikes. The only way to get replacements like that now would be to scrounge them from other carb sets of the time. In your case, the '78-'79 BS38s came with no-hole 27.5 VM22/210 pilots.