I think I would put the blocks in a draw and keep them there. I would replace the blocks with the bedding compound. It is a pretty tricky bed. The huge magwell and trigger areas make the job much harder. I had a similar problem. I used plasticine to fill the magwell and trigger area and all the little holes ect on the action as well. Then just bed the action to the stock. The bedding compound will take the place of the blocks and be an exact fit.
The other option is to glue the blocks into the stock and then bed from there. I think the gap may be to small if you go this way and the compound will chip away from the blocks.