High or low?
If the flow is 10% high, then it is probably an electronics/firmware problem and not really user adjustable*.
If the flow is 10% low and you have already replaced the check valves, the next thing to do is a "leak-down" test: connect the outlet of the pump to a plugged union, set the high-pressure shutoff to somewhere near the upper end of the pump's limits (typically, 4,000 - 5,000 psi) and start the pump. When the pump shuts off, start a stopwatch and monitor the pressure. At the end of 15 minutes, the pressure should have decreased by no more than about 10-15%. If the decrease is greater than that, there is an internal leak in either the seal(s) or the inlet check valves. If the pressure holds steady, then it's an electronics/firmware problem per the first paragraph.
* it may have to do with compressibility compensation, but I don't know if that's user-adjustable on that pump.
