I am dealing with the same problem right now. I have a '04 CRF 50 with the same filter and all of the same things you are talking about, removed arrestor and changed the needle position. I have changed the main jet from a stock #58 up to a #65 this seems to have helped the top end not to miss.
However...I am not sure if the #65 main is big enough because I have moved the needle clip to all positions and it is still bogging at 1/4 to 1/2 throttle. I plan on moving the needle to the 3rd clip and going up again on the main.
Please let me know if you have any luck with this problem and I will keep you informed on my progress.