BMW's are notorious for being very picky when it comes to electrical power. I can't say for sure that a bad battery caused those exact faults, but it isn't out of the realm of possibility. Electrical gremlins do all kinds of strange things to modern BMW's. It's been documented across multiple model forums since as early as the E31 and E36 onward.

I would clear the codes and replace the battery if it were me and see if anything returns.

Theremostat failures are very common on this car. Along with boost hose, vibration damper, vacuum lines, emissions, glow plugs/module, engine mounts, cbu, etc. The best place to find info on these engine problems is e90post. N57 / M57 Turbo Diesel Discussions - 335d - E90Post - BMW 3-Series (E90 E92) Forum

So there are three major components that fail in the SCR system commonly. The SCR catalyst, which can plug up because of soot or urea crystals, or the catalyst wears out. The SCR urea injector which plug from cystlized urea. Finally the DEF tank, which has a common temperature/heater module failure (which can be fixed by using the VW toureg module).

The SCR's don't fail from low engine temperature (or at least not that I've seen). Low engine temp causes the glow plugs, glow plug module and often the DPF to fail. As when the engine fails to go over roughly 80C it keeps the glow plugs on which wears them out faster. Also with low engine temps the DPF will not do a normal regen and can plug up with soot. Causing a failed DPF and the infamous reduced power warning.

The NOx sensors fail frequently on this car and can give the false indication that the SCR is not working. The typical test is to either replace both NOx sensors or swap sensors. There is also a sensor test that can be activated.

I've had all of my emissions equipment replaced at least 1x, tuning and deleting has its downsides too like more noise, diesel stink, smoking (potentially), not resalable in emissions states, and its not cheap.

Wouldn't the engine running that low cause a bunch of fuel to be burned and hydrocarbons into the exhaust? I didn't have ista set up when I went into limp mode unfortunately.

That is the right part right? Can someone also explain how to delete these codes individually?

Battery seems to have been replaced last year. Bosch 49-850b. Looks like it has 120 amps. How do I made sure the proper coding was done?

So injecting fuel into the exhaust is done on purpose in these engines. The cars do post injection events (inject fuel when exhaust valves are open) to send unburned fuel into the exhaust where its is burned by the Diesel Oxidation Catalyst (DOC). The point of the unburned fuel in the exhaust is so combustion takes place in the exhaust stream raising exhaust gas temperatures high enough to burn the soot captured in the DPF. So by design these cars are intended to operate with unburned fuel in the exhaust as part of their normal operating process.

The DOC and DPF ensure that minimal residual fuel and soot are left in the exhaust by the time the exhaust stream reaches the SCR. The SCR doesn't have an issue with unburned fuel per say its bigger problem is having its passages clogged by soot, which is why its located post DPF. Also it can't handle sulphur either.

BTW if the DOC wasn't working on your car you would have bad diesel stink exhaust fumes, like making your eyes water bad. So all of this was a long way to say, I don't know why your SCR failed, but low engine temps don't kill them as far as I've seen. They kill DPFs (don't get hot enough to regen), glow plugs and fuel economy (engine doesn't leave warm up mode). My car has had its SCR injector, Catalyst, and DEF tank all replaced at separate times and has not had the thermostat fail. SCR failures are not uncommon on BMW diesels.

So I'm in the middle of doing injector 6, should I post a DYI with pictures? It was fairly straight forward. Biggest challenge was removing the injector. Once I broke down and bought a slide hammer it took about 5 seconds.

Did you get Rheingold setup and working?

From there, you can:
-Reset injector adaptations. A must after replacing.
-Register battery.
-Delete codes from individual ECU(s)

Did you have a download link for rgold? That one could pm me

Is Rheingold that much better than INPA for the e70?

Don't have experience with INPA. Can't tell.