Hi Patrol,
No, I'm sure my 'off zero throttle' misfire is not related to to the fundamental set up. Until this problem had developed it was sweet & pulling like a train at all revs & throttle, with a 19t sprocket too. I had a swop with a fellow rodent's 98 TBS last weekend for ~ 25mls. I thought performance ~ same - he thought mine was quicker. His stock 6 speed setup is ~ 2 or 3 % lower geared, so maybe I do have a little more torque/ power.
My only other tweak is to file the ignition pickup mount holes to give ~ 2 deg more advance - my calc is .65mm 'circumference' length per degree.
I'm of the opinion that the stock airbox (with a K&N) is the easiest way to go for strong low & midrange torque, while getting more top end - this is what the TBS has with it's extra 14 hp. The other (only) key difference with TBS is the exhaust balance pipe fitted at the muffler end. To me, this makes it look pretty much like the 3 into 1 I have. I suspect this is very significant - improving 'scavenging' - tho' I'm totally the amateur engineer here. (Have electrical eng. BSc but not much help with this !)
I'm not familiar with the emgo pipe, does this use the stock headers ? If it does, it might just be different enough to mine (or a TBS) to need a slightly different carb (or airbox hole?) set up.
BTW, I've just ordered an optional baffle, 'DB Killer' <not too much I hope

> from Thunderbike, & noticed they have a special offer on just now.....good value imho, tho' still bucks alright.
I tackled the 'duckbill' filter this morning & found about 1/8 of crud filling the bottom. Didn't look that much, but when I connected my remote tank set up to recheck carb balance, the flow through the clear filter was massively more rapid than before. So, I'm hoping....not tried it out yet as weather's a bit rough here too.