Good on you, you fixed them!
On a side note, I see the damping set up is more complex than I thought for this bike. Its kind of like an older ST1100 set up. One fork has a damper rod (it has the longer preload spacer), the other side is a cartridge set up. The shaft inside the spring is connected to a piston that will have a shim stack; there "should" also be a piston at the end of the cartridge - cool! The shaft is fixed mounted to the cap at the top. As the fork compresses, the piston moves up or down inside the lower cartridge. Given they are different, it will matter which new fork stanchion you used on each for what side as the bushings for each stanchion has to match up to the damper rod or cartridge. Did you remove the aluminum end cap at the bottom of the cartridge side or the top side of the cartridge during the disassembly? Did you have any other pics?
Do you know what the factory oil recommendations are for each fork leg? The oil weight and/or fill volume may be different for each fork leg.
There is great potential to tune the front end to be a much better than stock set up if you are a solo rider (springs and damping set up).