You said you re-surfaced the parts, does that mean there were more scratches after you surfaced them last time?
Air should self purge. I found my lift was shuddering and the wheels didn't move rite away when i did mine. But after running it then shutting down, pilling the rams in and out to get oil moving a little more, the wheels started to rotate. I have always found the drive system to be less problematic with air in the system than the lift and tilt. It must be the style of pumps used, vane pumps hate air bubbles.
How long have you been running it?
The way i have always done a run after pulling a pimp is to have it blocked, start it and pull the levers forward or back, just let them spin for a little while, change direction. Then take it for a drive on flat ground and lift the arms and let them fall while moving. Let it sit for a few hours or come back to it, or even next day and repeat the process. It will take time to get all the air out. Letting it sit for a while allows the bubbles to burst in the oil tank and you will have nice fresh non foamy oil to draw in. This will continue untill all the air is gone.
It will self bleed, just give it time. I don't know why its causing so many problems with the drive though.... I'm not exactly sure where to advise to go from here. Everything you have done sounds correct.