what about the strainer on the return side? if there is one? i wouldnt suspect its su ck ing (had to edit hmm) air
maybe a pinched return hose causing a cavitation?
try taking off and cleaning the hydraulic cap and breather element
run it with out the cap (if you can)

heres a slightly different situation but im sure it can apply in reverse
i had a customer with a diesel that would die on occasion
he had the pump and injectors done with no success b4 calling me in
the 1st thing i did was open the tank and i got a huge "whoosh" of air
he had replaced a vented cap with a nonvented cap and the vacuum buildup was enough to overcome the lift pump pressure with half a tank
new cap no problem

maybe the tank is having issues venting the air pressure as the cylinder lowers and the fluid level rises
far out but sounds like you looked at everything else already