Don't read too much into the exhaust note. It could be just a little lag between the time you open the throttle and its reaction time. As regards using a fuel management system, any free flow exhaust system makes your vehicle run lean......meaning it gets less fuel than needed. This in turn leads the engine running hotter than usual and can be the cause for a number of problems for the engine, and that's why, manufacturers void the warranty if you use after market exhausts.
In your case, with the removal the discs and the end cap, you're exhaust system has in effect become a free flow system, and it will cause the bike to run lean. Having said that, don't get too worried. If you are using the bike for short distances and city runs nothing will go wrong. If you are still concerned, go for the fuelpak 3. All your worries are over except shelling out a few extra dollars.
The FP3 is an OK fuel management device It has a lot of bells and whistles on it IE bluetooth etc.
If you do not have a good Dyno tuner in your area it is a cheaper option The Super tuner also has a smart tune option. Both will get your bike to run OK.
When the bike is Tuned on a dyno with a good tuner he will correct the Volumetric efficiency of each cylinder at all throttle positions and RPMs whereas the FP3 and SE smart tune feature will get you close.
The Supertuner is the only device that will allow a Tuner to make permanent changes to your Fuel / Ign timing and more MAP in your ECM.
A piggyback system will be constantly lying to your ECM to make changes after it has determined that the fuel values are not within parameters.
Bottom line as I dont want to make this long winded (I am not trying to promote HD stuff Only what I know from experience works)if you Do Not have a reputable Dyno tuner in your area go with the FP3 (it will get you close.
Something is better than nothing an exhaust pipe change is Huge.
We ran a bike before and after having a FP3 and V&H Pipe installed and it gained only 3-4 HP.
I gave the customer a hefty discount to install the Supertuner,which he did ,he has to come back for the tune as he had an accident.But I will post the results as soon as I get them.
BTW Supertuner is at least double the price of a FP3.