It seems to me like your first problem is the different combustion chamber volumes. If the cut was at an angle, lengthwise, then first, you will have to re-machine the deck square to equalize them.You really don't want a different compression ratios in each cylinder. Your rocker shaft pedestal height will all be the same and can be shimmed equally. There is quit a bit of adjustment, are you saying it's all used up?! There should be enough material in the head to cut the intake valve seat to the original position. Don't forget lash caps are on the table too. In the old days folks routinely whacked 1/8th inch off these heads and I personally have came close to that, although, for racing I zero decked the block along with notching the pistons for valve clearance. If you can not re-machine this head, you will need to find another or have a very Micky Mouse set up.
