Ok, well Im going to drain the brake system and clean the crap out of it and refill with DOT3. Well it came with 4-2 exhaust but the mufflers/baffles were 1-2 split, so not really 4-4, more 4-2 with dual outlets on either side. The stock V-split mufflers have been replaced with Magaphone style pipe ends. The stock jets that are in it are 100's...!!! This bike must have lived a previous life in high altitude...now at 600 ft, should I go with the 115's??
What color is your present brake fluid? If it is purple, then it is likely silcone based DOT 5. This is in no way compatible with DOT3 fluids and is near impossible to thoroughly flush from the system, as nothing dissolves silicone. If you do have DOT 5 you're pretty much stuck with continuing its use, unless you dismantle the whole system, replace all the rubber bits and Flush, Flush, Flush.
If you are arguing that Honda produced a stock CB550 with a 4 into 2 exhaust system, then I dare you to find such parts in the part list.

But, I warn you, they don't exist. The F models (introduced for 1975) were all 4 into 1 on the showroom floor. The K models (including 1974 offerings) had an exhaust per cylinder which extended from the exhaust port to the exhaust muffler end, making 4 distinct inlets and 4 distinct outlets. Aftermarket suppliers did produce a 4 into 2 slip-on system (I assume this is the " Vsplit" you speak of), which used the existing head pipes with the four mufflers cut off. I had/have such a system, purchased in 1975. But, there is no way these can be considered "stock". There were also other manufacturers that produced entire 4 into 2 systems for the CB550. But, it wasn't Honda, and therefore not "stock". It is not surprising that your bike doesn't have the original set up. The original mufflers often rusted out in 10-15 years and had to be replaced. Few would spring for the $700 Honda wanted for new replacements. The entire CB550, when new only sold for a little more the twice that. For about the same price as one muffler from Honda, you could get an entire exhaust system from other suppliers.
As noted in the FAQ The stock main jets are #100 for the 022a carbs. My 74 ran great with jets both with the 4 into 2 and the 4 into 4 exhaust setups. But, I use the stock airbox and a Uni NU-4055 foam air filter. I don't think Honda sold anything different (jet-wise) based on destination altitude. If higher elevation tuning was done, it was done by local dealerships. I never saw any Service Bulletins or notes from Honda regarding mixtures changes for altitude, though it is certainly true that altitude effects ideal combustion mixtures in these bikes.
Cheers,