I have the same exhaust on my 250 ETZ and without any modification on the engine (except for lightening and balancing the cranckshaft and the clutch but it is not expected to improve the power) my engine is able to reach 7000rpm very quickly and easily. And since I had removed the air filter for a K&N one and modified the air box cup and increased the advance, the engine is linear from 3300rpm to 6500rpm. I remenber I've modified too the needle position in the carburettor, I put it on the poorest level.
I don't think that your exhaust is too ambitious for your engine, I suggest you to check your ignition point, and to optimize the needle position. Then, if no change, you could drive your motorbike without the airfilter and its cover just to check if there is a change.
The other avantage of such an exhaust is the wieght : may be you save 8 kilos from the guenuine one! Is is worthwile... Ant it is a beautiful expansion chamber exhaust. So, you could try to keep it and to check all the other elements... Moreover, you will gain in comsumption. despite the accelerations of my 250 ETZ, I am capable of consumming less than 4,5 liter/100km (excuse me I am French, I am not comfortable with gallons and miles
when I am not fast. Otherwise, I am around 4,5 l/100 in riding at 100/110 km/h...
All the mods I implemented on my ETZ are described there below (I have last started to adapt a reed box from Huqsvarna in order to increase the torque). Even if my engine is entirely new, you can make sure that what is described there is efficient. I am sure something is wrong on your engine either on the ignition, or arount the air filter and its cover, or on the carburetor's needle... Or both...
http://strv.pagesperso-orange.fr/motodesign/UKETZ.htm