Do as FOG says and you'll be on the right track to squaring up your carbs.
However, by your description, it may be hard to admit, but your carbs just aren't 100% clean yet. I'm also getting the feeling you're in a bit over your head.
First step, take a deep breath and relax, take a couple days off of working on the bike. Give yourself the chance to think of something other than a motorcycle giving you a headache for a bit, and do some research (which is you've started doing by posting up here) on some solutions.
Custom Carb Services (aka Ducatiman) knows his stuff. He can either rebuild your carbs or walk you step by step through the tried and true method of properly rebuilding and tuning these carbs. FOG also has extensive experience with carbs and I've been into the EX carbs numerous times as well, so we can all help set you right. This does mean you have to forget whatever it is you've done to the carbs up to this point as it definitely has not solved the problem.
As for your petcock, rebuild kit is great, though get yourself a factory OEM vacuum diaphragm. If you're using the one out of an aftermarket kit, throw it in the trash. Trust me, it will give your problems later. I've tried a variety of aftermarket vacuum diaphragms on these petcocks and they all fail on short notice. OEM is the only way to go.
1990 EX500 - 140,000 miles as of May 27th, 2019
1993 Ducati 900SS - The real canyon carver
2002 EX500 - Undergoing a full restoration