Hmm, did you use this page from 250 FAQ?
https://faq.ninja250.org/wiki/Replac...6_brake_levers
It's just one bolt to remove lever and one bolt to re-install. None of that stuff had to come part. Although it would make procedure easier if FAQ mentioned to loosen clutch-cable adjuster down by engine as well. Issue you have is you don't have enough slack on choke-cable and it's pulling choke-lever and cable-guide together and overlapping them, making re-assembly difficult.
Best to disconnect choke-cable from carb to have plenty of slack. Then it'll be much, much easier to re-assemble. You want to line up the channel that cable runs through and connect them between pieces. Then it'll make sense how it all goes together.
First, disconnect choke-cable from carbs:
https://www.ninjette.org/forums/show...41#post1280141 . This can be done from side of bike without removing tank or carbs (don't be tempted to remove and lower engine). Might as well lube choke cable while you have apart.