Quite often there is confusion between the amount of oil and the level of oil. It doesn't matter that different oil amounts are in each side. The level from the top is stillidentical on each side. The different amounts are to compensate for the additional components on each side but in the end the levels will be the same. If you know the level then the amount wil be taken care of and becomes irrelevant. If you read the link I provided above, all the info is there. The only thing to be aware is that the level for 88-94 is different from 95-00.....Ther are 2 different oil amounts for the forks on the 1500. one is for the side with the anti-dive valve and one is for the side with. don't remember off hand.
You need to drain the forks and replace the fluid with ATF, as in the service manual.