front two holes on both sides
My 02 4wd swb 6spd had the rear sway bar removed by the PO. I got a sway-bar, links, brackets, etc off a scrap-truck at the wreckers. On both sides, the U-brackets were bolted to the forward two holes, and yes, on one side I had to remove the lower end of the shock absorber to get the bolt out. When installing on my truck, I used the forward holes.
I don't think it would matter if you used the two forward holes or the two rearward holes, I think what you want is the vertical links at the front of the sway bar positioned as close to vertical as possible, and the effective radius of the sway bar to be the same on both ends. I'm not sure, but maybe 2wd trucks with lower ride height use different u-bracket mounting holes than 4wd.
While you're at it, check the vertical link on the front of the bar, the lower joint will get loose/worn over time, the lower joint seems to be the wear point. On the one I got from the wrecker, the links were both pretty much new. But there were a couple others at the wrecker where the lower end of the link had wiggle-play, which would translate to rattling over bumps.
Having driven mine both with and without the sway bar, I don't feel any difference, in either sway or ride harshness. All the driving I did was empty. If I was driving loaded (I mean with a load on the truck), especially a high load like a sled-deck or camper, sway might be an issue.