The transmission pump problem should not have an effect on high pressure hydraulic functions. They are totally different system, sharing only the oil. Only possible connection is if the transmission pump is aerating the oil to the point of causing the Hydraulic charge pump and high pressure pump to cavitate... Although on second thought, the air pump in the transmission pump does keep oil levels in transmission housings correct during operation by pressurizing housings. Possibly could be getting low oil level around sump screen during operation causing cavitation. I have never had an air pump fail to see the results of a non functioning one.