how much the aftermarket exhaust affects the engine depends on how radical the exhaust is
A slip on 'muffler' that is just louder but still has some baffles wont affect the engine much by itself. It will barely increase the HP, and you can often get away with the stock jets.
To get a noticeable increase in HP you have to also open up the intake air filter and plumbing. Then you will need to change the jets and the PMscrews to allow more gas to match the increased air flow thru the engine.
There are lookup tables for different intake and exhaust mods that will tell you which jets to use and how far to turn out the PMscrews.
If you put straight pipes on the exhaust, no baffles, then you can lose HP. It gets complicated at that point.
You should be able to get a good read on how well the jets and PMscrews are set looking at the plugs, if they are fouled out black, or if they are running hot and look like they are melting...melting... oh my world...what have you done?
Having said all that, if the bike was running ok for the last two months and now it seems like the performance is degrading, there has to be something else going on.
EDITED: looking back,... the bike is a 2006 stratoliner. Im not sure if it has carbs or fuel injection. If the bike is fuel injected then you need to re-map the ECM to give it more gas, or have it flashed with a new map by one of the websites that does this, to match the exhaust and intake/air filter on the bike. But still, if it was running ok last month, that should not be the issue.
Last edited by KCW; 07-31-2018 at 02:09 PM.