The proper way to check hyd oil level is with all outriggers up, beams retracted, boom in the rest, with all sections retracted. Tank level should then be in the middle of the sight glass. If you have no oil in the retract lines, or the in the other side of the cylinder, it may take the oil a little time to get it filled enough to start retracting, and oil must get to the check valve to open it up. The second sections oil travels from the valve, through all the hose in the hose reel located under the rear of the boom, then to the section. It's a pretty simple system. Follow the lines from the control valve onward. All that system has to be full of oil before it works, and you've had oil level issues.
Also that grove will be boom heavy. If it hasn't seen a lot of maintainence , I wouldn't scope it out flat and try to retract it. Boom it up over at least 60deg. then try to retract it. If the boom is really dry on the bottom of the sections, it won't want to retract.
You can look at it this way. To move the boom section, you need the oil to flow there. Are you getting oil flow to the retract of the second section? Crack lines or feel/ observe for movement in them (oil will make the hoses jump). If no oil, figure out why. If you are getting oil, either the section itself is giving you too much resistance, or you aren't getting enough pressure. I don't think that's likely- there's enough pressure there to extend it. Did you cavitate the new pump? (running with no oil, low oil in the tank will cavitate/ heat up the pumps, ruining them. Don't do that.)
I don't think you've cooked the new pump. The oil pressure that is extending the boom, is the same oil and pressure you use to retract. All you do is throw the lever the other way. Either you haven't held the lever long enough, to purge the air from the hose and cylinder in the retract side of the cylinder, or your boom is just binding up. Boom it up and give it a little time to fill with oil (holding in the retract lever). If you see the boom start to retract, then stop, you probably have oil there, and something else is stopping it. You will need to throttle up to retract. You have to provide enough pressure to release the holding valve, and overcome the drag of the boom.
It's possible your damaged pump has sent steel through the system, and a piece lodged in that holding valve, locking it so it won't release the oil from the bottom of the cylinder, but I doubt it.
I think you've just not got the air out, because you said you had no movement of the second section, then added oil and now have extend, but no retract. Also, don't extend that boom all the way out and flat over the side, only do one section at a time for greasing, it's a little boom heavy to put it all out over the side flat.
Good luck.
