Removing the "power chamber" shouldn't require re-jetting nor will it need the pod filters. That unit extends the primary pipe length to the correct size to enhance the lower rpm power band. Running straight pipes, depending on the length and diameter, will likely lead to reduced power. For the exhaust I would suggest using some lower restriction mufflers, they should have 2 liter internal capacity.
Have you verified that your ignition timing is actually advancing to spec? It's probably advancing late which decreases power.
When you rebuilt the engine did you use the original pistons or the higher domed ones?
If you consider that this is 400cc's getting 43 HP when everything is right you've got plenty of power for the size, plus reliability and good fuel mileage. Compare it to a 302 Ford, 5 liters. Does that get in excess of 500 HP with good fuel mileage and long term reliability using carburetion. No.
Now if you really want to get as much power as possible from the engine you'll need to do things like make a tuned 2-1 exhaust system with a low restriction muffler, use the higher compression piston, 5 or more angle valve job, ceramic coat the pistons and combustion chambers, probably a cam change as well. I've done the above with the exception of the combustion chambers and cam. Not only is it faster than my Subaru, it gets an average of 58 mpg and will cruise all day long at 75+
+1 on what Jim has said. Hondas are tuned to a high standard from the factory. What you are talking about will un-tune the bike. It takes a huge amount of highly skilled work to get more out of the bike.
The exhaust side is tuned by the header pipe length and diameter. The theory is; when the exhaust valve opens, a pressure pulse starts down the header tube. When the pulse hits the muffler, a low pressure pulse shoots up the header back to the valve. The trick is to time the low pressure pulse to hit the valve at the exact time the valve starts to open, this puts a lower pressure at the exhaust valve. It has a supercharging effect, and is sometimes call being on the pipe. There is a RPM range when the pulse hits the pipe ( this is a timing thing through the 720 deg four cycle). The larger diameter the pipe is, the tighter the RPM range is. A smaller diameter pipe has a wider rpm range but more back pressure, a larger diameter pipe has a tighter RPM range. A shorter pipe will time the pulse at a higher point in the RPM band, a longer pipe puts the pulse at a lower RPM band.
The intake has a similar effect. The difference is the intake gas flow is interrupted by the intake valve closing. When this happens, the inertia of the gas flow builds up pressure behind the intake valve. the trick is to time the next engine cycle's intake valve's opening exactly at the time of the maximum pressure point. The same theory regarding exhaust length and diameter apply to the intake, the difference is on the intake side restriction is the culprit, not back pressure. The length of the intake track runs from the intake valve seat, to the end of the intake tube in the air filter. POD filters shorten the intake tracks a lot.
These are just a few things that will be affected. Motorcycle racers use things such as exhaust gas analyzers and dynometers to measure the changes. Keep in mind this is only part of the equation. Gas flow through the head and cam profiles affect the engine RPM band too. All of these need to be matched, intake, Cam and exhaust to the same RPM band.
Good luck, and let us know how it goes.