I have a '98 with a leaking rear axle seal. Since the bearing has been compromised with gear oil, I'm looking at replacing the whole axle shaft assembly (with bearing) with a non-leaking used one (about $50 at my local pull-a-part)...

My concern is that I've read that there is a revised version of the seal that contacts the shaft on a slightly different location, resulting in leaks. I'm hoping someone can verify this, and hopefully either find a workaround, or identify a seal part number that fits the same as the original seal...

I don't follow. Leaking seal needs seal replacement. And to be prudent, replace the bearing.
But this doesn't justify replacing the axle shaft... unless you suspect it is bent, thus causing the seal problems.

edit: Or are you saying, since the whole assembly is only $50... why not?
I'd suspect the bearing and seal condition on the salvage part, and still want to replace those.

The seal needs to be replaced with new, but I'm getting conflicting info on model numbers and how well they fit the shaft in the stock retainer spacing...

The axle/bearing design on these isn't conventional; instead of a bearing in the axle tube that is lubed via oil bath, there is a seal between the bearing and axle oil, and the bearing is lubed with grease. When the seal fails, gear oil flows through the bearing, contaminating the grease, compromising the bearing.

The bearing and several other components on the axle are pressed, and not a quick job; everything has to be cut off the shaft and re-pressed on... The result is a $1k-1500 job, and I don't have the time or equipment to do it myself. This is also a secondary vehicle that I use for launching a boat on a beach, so I don't want to spend a lot of money on it.

So, I've found a low-ish mileage (under 200k) wrecked 4R, smooth, not leaking, which I can swap the shaft assembly from in about an hour, for about $50 + the new seal. I just want to use the original seal design, if possible, because I won't be able to manipulate the retainer position. I'm not trying to salvage a seal, it needs to be new.

Watch both my videos and you'll know more than most paid mechanics about this subject. Also read the comment I pinned (1st comment you see for updates on the job).

In Part 1, I used a toolset I no longer recommend for the press work. When it comes time for the press work, use the axle toolset featured in Part 2.

somewhere I read that the napa seal follows the old design and will hit in the correct place. I do not know for sure. but if someone had an old oem and took it to napa they could find out

There is a massive thread here on this very topic.

Rear Axle Seals: The Ultimate Information and Replacement Thread (3rd gen)

But if you pull the axles yourself it shouldn't cost more than 100-150 per side to have them done at a reputable shop. Then all you have to do is the inner seal and brakes.

I have not done it myself but its on my "must do before winter" list.

I did this for my uncle's Sequoia since he's cheap af. That seal wasn't redesigned though. AT minimum you'll need to press on a new retainer is you intend to use an OEM seal. Otherwise go aftermarket seal.

Maybe next time for the other side, but I already have the 144k mile axle, complete with brakes, ready to go in for what should be a quick, easy job. It's looking like doing it with all new parts and having a shop do the pressing would still run $900+, in addition to a lot more time... a lot for a secondary vehicle. If I get a seal that matches up, I might even grab the other side of the donor truck to have just in case.

You could get the press and tools now and press a new retainer using the flip method on that axle you have. Then later you'll have the tools to do the job right. I personally wouldn't trust anything but an OEM seal. Yes it sounds inconvenient but so is redoing the job.