charge the battery back up with the trickle charger and see how it takes the charge. You need to a determine how good the battery is at this point and you'll need a nice strong battery to help get the bike started, anyway.
when you cleaned out the carbs, did you remove the pilot jets, clean them out and
also blow out the passages in the carbs with compressed air that the jets connect to? sounds to me like your pilot circuit is still clogged up. I'm not a fan of reaming jets out with wire and prefer to replace the jets with new ones if there are blockages in the jets that don't come out with a soaking of solvent and a blast of compressed air.
set your float level back to the stock specs.
have you double checked the vacuum hoses for cracks and made sure the are connected correctly?
when I purchase a used bike, the first thing I do before I start modding anything it is to make sure everything is working perfectly first and all maintenance is up to date to set a known baseline.
at this point you don't know if you're chasing a problem that existed when you bought the bike or introduced a problem from your mods and/or workmanship.
http://faq.ninja250.org/wiki/How_to_...e_your_jetting