I may know what you're talking about. I have the same tractor. Check your 3pt hitch lever. Make sure it is not in the fully UP position. If you leave the 3pt hitch lever in the fully UP position the hydraulic motor will whine, and the system will heat up. Whining increases when cold. This situation will cause the hydraulics to whine continuously until you move the lever down and release whatever pressure is building up in the system from this condition. I have learned this over time operating this particular tractor. Whenever you hear the whine, reach down to your right and adjust this lever to break the tension. Always leave the 3pt hitch lever 90% of the way raised if you want to avoid damage/overheating to the system. I don't know why it does this, but that's what mine does and the symptoms sound similar to what you're talking about. Try that and see what happens.
I have always noticed air bubbles in just about every hydraulic system I own. I think this is normal if the machine has been operating but I'm sure someone on here knows better than me.