Stock carb. Stripped and missing

I bought the bike from its second owner who had little knowledge of the bike and why it was not running properly. After procuring this beast , I removed the carb and discovered a 125 main jet sitting in the float bowl. After more investigating I determined the bike was fully uncorked and the mechanic who did the carb rebuild must have just put all original components back. Smog delete, unrestricted exhaust tip, high flow manifold etc.

My local shop did not have any pilot jets and the closest main i could get was a 168. After a cleaning I put the 168, threw it back together and voila. . . kicked it over, she roared to life and I learned what all the hype with the BRP was about. She was ripping but needed tuning.

As it sat it had a 168 main and a 65 pilot. I needed to take it apart again today to get that information so I can order the correct 68s and try the 172 or 175 as well as check the needle. Come to find out, the screw that holds the the shaft/needle together is stripped and does NOT want to come out so whatever is in there might be staying in there. I also discovered there is no jet bowl/holder. The bike seemed to run pretty dang good without it. What exactly is its function, besides its name. Could it have been removed as part of the uncorking process or is it vital for carb performance. I was surprised to recall on the bikes overall performance when I found it was missing.

Jet bowl holder: Are you talking about the main jet holder?

shaft/needle: are you talking about the screw for the baffle plate?

I am not sure what parts are you talking about sorry , but i strongly recommend that you check your carb and compare it to the exploded diagram from the service manual and find out what parts are missing , next step put them all back in as everything is there for a reason   

I think I know the part you're talking about.
It sits above the main jet, a sort of 1\2 hemispherical shaped piece that is attached via the main jet.
Most probably there to prevent slosh or turbulence below the jet in the bowl?
Won't stop it from running, as you've found out..
Personally if its not there I wouldn't worry too much.

Maybe using the uncorking guide might help ?
http://www.xr650r.co.uk/service/carb/carb.shtml

Zoro is spot on. I had to order a 68s from my local moto shop so I ordered the bowl/jetholder while I was there. It was 7 bucks so I figured why not throw it back in and see how she runs. On a secondary note. No fun if you lose or damage the nylon washer that fits around the throttle valve arm. You have to buy the whole assembly for $70 if you want the .16 washer. Mine was cracked and It was a bugger trying to find one with the right dimensions. Ended up finding one at Lowes but had to spend a little while on the grinding wheel with it. Every screw has been way over torqued and a pain to remove. I had to drill out and use n easy out to get the screw that holds the throttle valve arm to the throttle. . Gotta wait for that to come in also. . Plenty of time to ensure all the shavings and chips are gone and its spotless!
Happy Easter