I would add new oil, cycle the forks a few times, drain, and then refill. Just to be sure any contaminates were out. I know you've had this apart, but a little wasted oil to flush things one last time would not hurt.
Also, if you have not refilled yet, I would suggest using ATF instead of fork oil. I used it in my bike, the seals quit leaking, and it rides nicer. I still have my new seals on the shelf and might actually use them some day.