So, the theory was that one of our air issues was caused by the low friction seals in our rams, hence the strip down, seal re-placement and re-build. Well it wasn't the seals.. the air is still a problem, but the cleg control hasn't been effected by the use of standard friction seals, so I guess we have learned something from the seal kit change.. and wasted time and money!
Next we have a series of possible fixes suggested, we though it best to try one thing at a time:
1) Add a check valve in to the return line back to the pump. This had no effect on the air issue.
2) Lift the pump/tank up above the height of the manifold block. This had no effect on the air issue.