If your bar is 3/4" thick, I wouldn't worry too much about losing thickness by flycutting both sides. I don't think you would need to lose much more than 0.01 - 0.03" getting your bar flat on each side unless it was really warped. That is not much in comparison to the 3/4" thickness.
I would just flycut a smaller piece that you have already cut off instead of the whole length to see how much is really necessary to take off.
If you don't want to deal with flycutting, take one of the cut pieces and sand it with 220 grit SiC sandpaper and water or even a stationary belt sander (if you have one) to get it pretty flat before machining.
You want to true it up before machining any O-ring grooves or channels into it. Flycutting would be fastest and best, but this also depends on your equipment and experience.
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