Thanks for the info, there are actually three manuals for sale near me right now within budget, but alas I need the buyback complete before I can move on anything. Is there any way to check for the SMOD problem beforehand? Did the Pathfinders of similar vintage suffer from this as well, we are also considering one of those but prefer the Xterra
I'm biased because I have a manual, and love it, but that is the way to go and have no worries over the transmission. They are easy to maintain as well, every 30k miles just drain and fill like an engine oil change, just a bit harder to reach the fill plug.
Clutch life varies, if it has not been replaced and has north of 120k miles or so, you might be looking at replacing that, but with a manual once it's replaced you are back on the road for a good long while. Xterra clutches get the reputation of being weak, I don't necessarily think that is so, they just don't tolerate abuse as well. So if the previous owner knew how to drive a manual, it's not so big a deal. If the previous owner let their 16 year old kid learn to drive in it, that's another story. But you could probably feel it out and get an idea if it's in good shape or not. Just have in mind the possibility of replacing the clutch and it might not be cheap if you have a shop do it.
The biggest danger of SMOD I'd guess would be shoddy repair work. If you test drive and it shifts funny that would be a red flag. If there are records, or you can visually tell the cooling or transmission systems have been worked on, that is suspicious. The most dangerous scenario is someone noticed it early, did their best to fix it by flushing it all, but you still have junk in the transmission waiting to cause havoc at a later time.
Checking the fluids, both coolant and ATF, would show if the two are intermingling at the time you check. You would have to be lucky and catch it before fluid was changed. SMOD stands for Strawberry Milkshake Of Death due to the fluids taking on the appearance of a strawberry milkshake when they mix.
Prevention is much cheaper and relatively painless. If you get an auto you want to make sure this has been done ASAP. You can either get a new updated radiator that has the design flaw fixed, or install an external transmission cooler that bypasses the radiator.
You can find a lot more info on thenewx.org I own a manual so this is sort of info I've skimmed in passing, take it with a grain of salt and verify elsewhere.
And yes I do think Pathfinders could be affected, I know Frontiers were and they all have the VQ40 engine. I'd check to be sure. To the best of my recollection, this issue got sorted out around the 2008 year model.