If the lower section is flat, switching over to 5/16" tubing would help. With only 20 ft of drop, you're only going to get 15-18" Hg AT THE TOP at best. Lower down on the slope you're getting proportionally less (at best). Did you ever check the vacuum level at the top of the lines or observe the flow in the lines? That would tell you whether you actually had any natural vacuum, or you needed to spend more time looking for leaks. Even very small leaks on a 3/16" system will result in little vacuum being generated. It needs to be VERY tight. Another possibility is that you had wood chips plugging up the tees and connectors. You'd be able to see that just by watching the liquid in the lines for a bit while the sap was running.
As someone suggested, maybe separate some lines with the trees on the top on 3/16" and those on the lower slope with 5/16".