Not all 550's are the same, there were changes made over the years. State you year and model. 4 into 4 tells me you have a K bike. All the years prior to the 77-78 model have the air box rubbers available from David Silver Spares in the UK.
Pods only have a possible performance benefit at engine RPMs above 8000, or so. If you plan to routinely rev that high and beyond red line then that may interest you. You can find used 550 engines fairly cheap.
The 4 into 4 in fine in my book, A 4 into 1, if properly designed for length and tubing diameter can provide and extra scavenge effect at high RPMs. This will provide a power boost, maybe 5%. So, again, if you plan to operate the bike above 8K RPM and beyond red line, a good 4 into 1 will would be attractive. The down side is the reflected pulses and shock wave from the exhaust of adjacent cylinders. interfere with cylinder scavenging at lower engine speeds. So, you actually get less low end and midrange power from a a 4 into 1 than a 4 into 4. A street bike actually performs better with a 4 into 4 for all around driving. It is heavier, though.
I find that using a Uni NU-4055 drop in replacement foam filter, provides less vacuum drop in the carb throats than the stock paper filter. This creates less pull on the carb fuel jets, thus leaning the mixture over the entire operating range.
I have not tried drilling my emulsion tubes for more holes. I'm content with the 45-50 MPG, I get now. I'm concerned that leaning the mixtures further, will cause operating temperature rise above what the cooling fins were designed to dissipate.
There is no fan, so motorcycle movement is required for cooling, and even this is effected by the temperature of the air. Stop and go traffic or operation in high heat areas (Arizona?), along with a leaned mixture, it seems would shorten the machine life, if not hole a piston. Experimentation has its costs, reward in not guaranteed. But, you can find used 550 engines fairly cheap.
Stock airbox (Uni foam filter) and stock exhaust seems to work best with stock jetting and settings of the carbs. However, I'm at sea level. I'd consider changes if I operated primarily at higher altitudes, where less oxygen is gulped per intake cycle.
I find the stock gearing pretty good for all around operation. 17 Front and 37 rear. I've had bikes with a 16 front and the acceleration improvement was noticeable. Of course the fuel mileage suffered and the engine revved more on the freeway. The engine is happy to rev up. But, the more it turns per mile, the less miles are available for the same amount of turns. Again, you can find used 550 engines fairly cheap.
It's a curious thing. You say you love the bike. But, you want to change it.
It will never be a modern sport bike or perform like one. I kinda like them for what they are... I've been called weird before, I suppose.
If you do the cafe thing it will only look different, be more uncomfortable to ride and become a thing to look at rather than ride. The counter to this is that making modifications can be a rewarding learning experience.
And, 550's are fairly cheap.
Cheers,
