I would get a M-ATV 370 HP C7 crate engine when one shows up in the surplus market again.
The issues I've seen with the 3126:
1. Engine oil pump's have problems with the idler design and at some point they changed the pump from a gear pump to a trochoid pump. Some pumps have a ball bearing for the idler and some pumps have a bushing that is fed oil pressure directly from the pump (thus unfiltered - another reason to keep your oil clean and install a bypass filter). When the idler bushing gets worn it leaks oil volume from the excessively large bushing clearance and drops oil pressure to the oil galleries and gauge. The number of design revisions to the oil pump speaks to the difficulties that CAT had with these pumps.
This video shows the issues. Note that this RV in the video below has 90k miles on it but the FMTV's with their stock gearing cruise at redline while this RV likely cruises at peak torque. So the extra 1000 RPM of constant operation seems to do in these oil pumps a lot quicker in our world.
2. Oil coolers warp and allow unfiltered oil into the clean side of the filter housing. This is compounded if the oil pump is making metal from the pump or the idler bushing. Decking the oil cooler isn't that difficult - any cylinder head shop can do this for under $100. Worth checking IMO.
3. The HEUI system relies especially on clean oil - see #1 and #2.
@ckouba recently experienced all these pieces come together into a very large repair bill (in terms of parts - he did all the labor himself) - HEUI pump, engine oil pump, oil cooler resurfacing, many hours of labor, etc. All of this at only ~15,000 miles on the engine.
4. 3126 engine blocks of a certain serial number range have problems with bell-housing cracks.
5. The ECM is not that common and of the ECM's I have worked with I have only experienced complete failure on 3126 units. I have not had a C7 ECM that was actually "bad". In addition the 3126 units are much less common and tend to be 3x to 5x the cost of a used C7 ECM. There is some talk of the earlier units having internal batteries that can fail and render them inoperable - I have seen dead units but I'm not sure if that was related to this. All the ECM's I've flashed have no memory of the date and time so it seems that later units either eliminated the battery or do not rely on it's function. I've been meaning to open one up and see if the battery is replaceable or at least remove it if it's dead so it can't leak all over the board.
6. The 3126 is the lowest production volume of the various FMTV engines. It's the first generation of the HEUI system and so the C7 benefits from the mistakes made on the 3126.
7. CAT came out with a pre-filter kit for the C7 HEUI pump - and it's only like $400 for the parts! Sadly due to the design differences between the 3126b HEUI pump and the C7 HEUI pump there's no good way to adapt it to the older design. The oil supply inlet to the HEUI pump is much lower on the 3126 pump so there's no space between the block and the pump to install it. For whatever reason CAT has not developed this pre-filter for the 3126.
Theres's also a lot of other changes and upgrades that the A1R trucks got that A1's didn't have. And in terms of the market the A1 and A1R seem to fetch similar prices mostly because new buyers aren't aware of the differences between the two so any truck that is 2000+ model year gets the same higher pricing because those are the trucks that Acela and other refurbishers and integrators focus on (Acela won't even buy A0 trucks). There's a big jump in terms of pricing from the A0 to the A1, but not a correspondingly high jump from the A1 to the A1R. So the 3126's are over-valued IMO and it makes the most sense to start with the A1R unless you specifically want the A0 for the "mechanical" engine - that's a whole discussion on it's own though and typically people making that decisions fail to realize that even the A0 has electronics for the transmission and is less reliable in several other ways that make this argument questionable.