There are a few things that make bogging worse, like removing the screen, too rich idle or needle, too lean idle. It looks like you've found more than a few settings that aren't working.
My suggestion is to stay close to the standard setting and evaluate- (disregard the cold options)
#40 pilot jet
2 1/3 turns (a little more than the instructions)
Red needle #4 position
#172 main with backfire screen.
Stock air filter
I'm not getting any bogging with this setting in my CRF250R. Make sure the air filter is clean and try the stock filter.
Let me know how it works and, if good, make only 1 change at a time from there.
Thanks,
James