Not sure I agree here,the fs 49 is really getting the signal of a 46 anyway,its got a necked down venturi around the booster. you just need to experiment a little with jetting,fs carbs hit hard off the bottom at wot bud,they have some other issues with little stuff in the mid range for rec riddin but hittn hard off bottom is their strong point.
I have riddin straight novi and fs 48s on a lim 701 setup that hit super hard.that said for these small motors I think 46s can deliver the same amount of power,for alot less $.But the 48s or 49s are not hindering it whatsoever jetted right.
If your cases are epoxy and ported,you might try stuffers. By high speed intake to you mean a boyesen intake with epoxy in to consume a little of the extra space to get a little quicker responce? Maybe try checking your timing with that flywheel and make sure you have around 24 deg static advance?