All is stock as far as I know except it has a 4 into exhaust system, don't know the brand, and I put a fuel filter in-line from the tank to the carbs.
Do you think re-assembly to the filter box will make a difference?
The filter box, and more importantly the stock paper filter, will certainly make a difference. It seems unlikely that your 4 into 1 has the same back pressure than the stock 4 into 4 mufflers. This means cylinder scavenging will be greater and more oxygen available for combustion. Carbs will need to provide more fuel to compensate.
So, be warned that while the stock filter should improve matters, but it may not be enough to restore full performance from the engine.
Don't forget to open up your IMS.
I doubt you're going to put the stock pipes on it, so I think you will have to face getting larger mains, possibly raising the slide needles, and getting larger pilot jets (or drilling/reaming the ones you have now), particularly if you run without filters or a lower restriction filter than what it had when stock.
Isn't bike engineering fun?
Cheers,