I put a yz 490 engine on an 02 ex frame I had the same issue, I made an intake. I cut the boot as short as I could with enough left to clamp. Then I bent some tubing and tucked the carb back in the corner almost perpendicular to the engine I used a spectra rubber cold air intake coupler from autozone to connect the pipe to the carb. Then did a similar process for the filter .....not sure how the crf fits but maybe you could lower the front mounts to tilt the motor more and do some stuffing.....my last idea would be to cut the frame, and weld in a circle for the carb to go through or a hump for the carb to go under or over. Theoretically this should support the frame as nessessery and allow clearance but I'm not an engineer lol.
Hope this helps.