Back in the "old" days, I seen something enough times to know it can cause problems, but never heard of it in this case though, I have seen where the spark was dying which caused a backfire or a plugged fuel filter.
However I learned from what my older brother always preached, if you free up the exhaust you must richen the mixture to compensate. Backpressure which is just held back exhaust gasses in the cylinder after the exhaust stroke occurs, so less of the air fuel mixture can enter the cylinder due to the left over exhaust gasses. So in turn the carb is tuned for that exhaust system, then you have the exhaust system changed over to a low restriction dual. Now the system is free flowing, there`s little exhaust gasses left over in the cylinder, but the fuel mixture is still set by the old system, so no more fuel enters the cylinder but more air does, so the mixture is dead lean, and the carb cannot compensate for it, it has to be jetted up to be corrected. I seen in extreme cases the mixture is so lean it burns the exhaust valves.
Now I`m not saying this is the problem, but I am saying this does happen, when I changed the exhaust on my three wheelers to cobra systems from the dead stockers, I had to richen the mixture to get the lost power back. If the fuel pressure isn`t up to snuff then by all means get it back in order, then I would check the mixture, you can bet it`ll be on the lean side.