Open headers with stock airbox = what size jets?

A little history on the setup first. I got a 76 Twin with open headers and a stock airbox. I rode it home about 20 miles with the "choke" about half way and it ran just ok but would blow black smoke when I laid into the throttle. When I got it home, it leaked gas heavily out the bowl on the right side. The carb boots to the engine side are cracked, so I know I need to replace those too. The plugs are bordering fouled. Currently has the stock jets 45 pilot and 125 main with clip set on #2 position. 2 1/2 turns out. I'm cleaning the carbs now and found a little piece of black plastic stuck under the pilot jet for some reason. Not sure where it came from. The gaskets on the bowls look fairly new but the bowl wasn't on that tight. Now here's my question: I've seen where a lot of people suggest it will run better with a 50 pilot jet. What size main should I run and where to put the clip? I'm thinking of fixing the intake, cleaning the carbs and putting a 50 pilot in to start and go from there but want to have some main jets on hand if I need to change them since I have to order the pilots anyway.

Well firstly, the condition of the engine and intake/exhaust and carburetors themselves need to be very good. no cracks anywhere or airleaks of any kind and good compression across both cylinders.

The jetting will not be too difficult a challenge if you stick with the origional airbox.

Riding the bike with the choke on is a NO-NO. This is the primary cause of fouling plugs and excessive cylinder wear.

Fix everything first, then start jetting. It is impossible to jet a bike with problems/possible air leaks.

Jets should be stock pilots, needle one richer and probly 1-2 sizes larger on the main - not too difficult.
Screws will likely end up somewhere in the 2 - 2 1/2 out position for highest idle point.

Take the time to do it right, else you'll be chasing all sorts of problems around for months.
Get the OEM service manual and perform the maintenence chapter. Firstly checking valve lash.

Good luck.

You can't tune it until you get all the problems fixed. Vacuum leaks on the intake side are a big problem. You need to clean the tank and install filters. Clean the carbs, and fix the flooding issue. You can get a Keyster rebuild kit for this carb and it's worth the money. Set the fue l levels in the bowl to the correct level. Once you get all the problems fixed, then you can tune the jets and needles.