There is probably far better advice from experts here and I'm sure you'll get other suggestions soon, but for starters - did you check the scavenge pipe before putting the crankcases together? if this is damaged or leaking then it wont draw its designed quantity of oil from the sump. I'm not sure how you can check this with the engine assembled but I am guessing you could push a tube on the filter end, block the oil pump drilling and see if it holds pressure. You say oil is returning to the oil tank and the pump is new, otherwise I would suspect the pump - weak spring or ball not seating correctly. Don't understand why the left hand cylinder is burning oil if you have rebored? Could you have snapped a ring on assembly? Might be an idea to add a comment on how many miles you have covered since the rebuild.