I'll soon be taking delivery of a 93 F2 with an unknown filter and a Vance and Hines full exhaust. I'm wondering what jets are standard with the stock filter and what jets are standard with an aftermarket one. Assuming sea level and 80 degree days.

 

The main jet on '93 stock carbs is a #135 with a #38 slow jet. I think the main jet was #132 on the California models.

I don't imagine there is really a 'stock' jet for aftermarket set ups. It's a case of trying a few settings and seeing what works for you and your bike.

I actually have a K&N filter and a Yoshi pipe but my carbs are stock setting. I took it to get new tires put on last week and the mechanic took it out for a quick test ride when they were on. He came back all smiles raving about how smooth the bike was. I took that to mean the set up wasn't too far wrong.

 

I was running a K&N and a Danmoto exhaust. I was all the way up to 145 jets and it still was running lean. A lot of people will tell you to forget a K&N as they're very hard to tune to these bikes. Even guys who had then dyno tuned still say they're not dialed in perfect.

Long story short I pulled the K&N that came with the bike and put an emgo paper filter in it.
I'm running 132 keihin mains with a factory pro kit. My needles are on clip 2 and my mixture screws are all 2 turns out.
Runs like a top but these bikes are all a little different. I'd start with like 130 or 132 mains and go from there. If you have a K&N I'd start at 142's at least. Motorcycle superstore has the jets for like $14 for a pack of 4.