I got mine to fit by using a shorty intake, then had to trim the stock air filter to get it to fit in there... Here's an older set of pics where I was using a CNS carb with an offset air filter duct, this gave me the clearance I needed but I ended up going back to the stock carb since it worked a lot better...
Here's a pic with the stock carb and I was going to put on one of those K&N type filters but it wouldn't fit, I ended up using a standard NT carb air filter but had to trim a little off the top back corner of the filter housing to get it to fit without touching anything else...
Kinda hard to see since I have no close ups of the stock air filter installed, but you can see where it looks like it's touching the top frame tube... there's only about 1/16" clearance if even that, and I had to do some trimming to get it in there... You can see the short intake manifold pretty well tho, this is the only way I had clearance to put the carb inside the frame...
You can try a shorty intake if you would rather keep the carb inside the frame, or you can go with an offset intake which also works. Personally I don't like the offset intakes even tho they are really good for adding momre torque to the engine's output, they do restrict the max rpm to under 6000.