Forgive me if I'm missing something but I do not see why you should have to fully submerge the wood to reach maximum penetration of the resin.
As far as I can tell, when in a vacuum chamber, air is pulled from between the structure in the wood and is replaced with the resin and that's great. However, if the wood was left floating in the resin (say half way) surely the vacuum would work more efficiently at removing the air in the part of the wood currently not surrounded by liquid. If this was the case, would the capillary action of the wood not draw the liquid into the centre of the wood more effectively?
Surely, if submerged in resin, once the first few millimeters of wood is saturated, it would take a greater force to remove the remaining air out from the deepest part of the wood as it would need to be pulled through the rest of the liquid whicg is exerting a greater pressure on the remaining air. My though is that if the wood was simply floating in the resin when the vacuum is initiated, once the piece below the liquid is saturated, the capiliarry action of the wood would draw the liquid up the rest of the wood more evenly.
Either way I will definitely be testing my thoughts on a piece of wood shortly but I would be interested to hear your thoughts.