I got A 2000 R* its has Speedstar BAK, Ported Manifold, AIS Removed, Cobra Slash cut Exhaust. Im getting the barons jet kit, what jet and needle setting would be recomended also is it recommended to get the larger needle and seat or is everyone drilling to out or leave it alone. I live in PA

There isn't any "drilling out" a needle and seat. Their a matched set. The taper on the needle matches the taper in the seat. Most people have been going to the bigger needle/seat, as a mod when going "pumpless".
You'll want to check the float level. Yamaha revised it, to match the 04 and later bikes. If it is still set to the original 99-01 setting, you'll want to raise it. Its a big change.
The Barons kit will give you a starting point, based on your mods. They'll probably suggest a 172.5 main, stock pilot(35), and the clip in the fourth from the blunt end of the needle. PMS screwed out about 2 to 2.5 turns from lightly seated(to start with).
If you haven't already drilled the plug over the PMS screw, there will be instructions, bit, and a sheet metal screw to pull the plug, in the kit. I would suggest getting the Baron's adjustable PMS needle(or something similar), to make fine tuning easier. It doesn't come in the Jet kit.
Read everything you can, in the Tech Articles, and doing searches on the forum regarding jetting, while your waiting for jet kit. Check for leaks around the intake manifold, and make sure that the "Coasting Enricher" cover on the side of the carb is in good shape(not cracked), and the plug on top of the manifold where the AIS vacuum line was installed is sealed up good as well.

I downloaded the instructions they are saying 170 main #5 clip with a spacer and one washer under the clip one washer on top and the PMS 3.5 turns out no mention of the pilot jet
And I did get Baron's adjustable PMS needle

do i leave the needle and seat alone i was reading one of the tech articles about the bike runs of of gas at wot

if it has all that, wasn't it already jetted? It should have been.

kxed wrote:
I downloaded the instructions they are saying 170 main #5 clip with a spacer and one washer under the clip one washer on top and the PMS 3.5 turns out no mention of the pilot jet
And I did get Baron's adjustable PMS needle

do i leave the needle and seat alone i was reading one of the tech articles about the bike runs of of gas at wot
If you read the directions it says thats only the starting point which means the bike starts and runs

It only had the exhaust I just did the rest. I was hopping some one had the same setup to give me some good recommenditaions so I don't have to keep guessing on the jet sizes

kxed wrote:
It only had the exhaust I just did the rest. I was hopping some one had the same setup to give me some good recommenditaions so I don't have to keep guessing on the jet sizes
click on my profile and click on jetting.

What air filter and exhaust are you using? Did you remove AIS

kxed wrote:
What air filter and exhaust are you using? Did you remove AIS
AIS has nothing to do with jetting.
Baron BAK which is an open K&N
Baron Nasties exhaust

I wasn't sure if the AIS would make a difference do you think your pipes would be comparable to the cobra slash cut in terms of jetting