You NEED to do more fiddling if you hope to get this project working; consider the facts:
You had two similar setups.
Both were working at the end of the night, and the boards had previously been used without issue, until some additional work was done on them..
But on this night, while both were working in the evening, come morning. both are now dead.
Chances are that when you try to wire up replacements they will suffer the same fate!
So you need to figure out what happened.
How much current was that setup drawing? CO2 sensors are often power hogs; some generate considerable waste heat; could that have been cooking something?... some LCDs can pull a couple hundred mA, too (colored high res ones, though the backlit character ones can pull IIRC close to 100 with the backlight on... How was it powered? Hopefully not from a wallwart through DC barrel jack if the current is high, though all those LDOs are supposed to be over-temp protected, it doesn't seem to work all that well. You seem to have two boards that are very different levels of damaged - one of them, I reckon is nearly working (the one that gives you bootloader flashes and then causes one of the serial lights to flash (did the code that was on it periodically print to serial?)
Did you have any places where a voltage higher than 5v could have been getting onto a pin? Or where a pin set OUTPUT might be shorted to the opposite rail, or a pin trying to drive the other way? or trying to power something that is too large a load for it?
The board that gives bootloader lights is a better bet. If the chip is removable, I'd try a brain transplant with a working chip. you can upload with the chip in a known working board, check if any pins are stuck HIGH or LOW - if so, whatever was connected to that pin(s) that are now blown is suspect.
If you can't upload via USB, can you upload using programmer? Maybe upload bare minimum so all the pins are INPUT, and check if any of them are actually behaving like outputs (that's the normal blown pin failure mode).
A REDBOARD is not an Uno. The serial; chip on the REDBOARD is more durable to electrical abuse than the 16u2 on the Uno (but not reprogrammable, not that most users reprogram the 16u2). My instinct is that an Uno would have failed faster, if any difference. mentioning it as a caution against thinking you should get official boards for better results as the replacement, and winding up with ones that are easier to damage instead.
