I understand having a busy time, I'm a father to two year old identical twin girls who have more energy than is possible and who get into everything they can. You can also explain the fact they didn't track the serial number due to the fact that didn't have access to that information on their ship. Once the returned to Earth, that would change.
You could also explain the chocolate as vets in the future have either treated dogs or engineered them so they have some sort of enzyme that breaks down the theobromine. That seems to me more likely since dogs have a habit of getting into anything laying around including chocolate. It also has a lot to do with the type of chocolate. Dark chocolate has a much higher concentration of theobromine than milk chocolate does. for a dog around Porthos' size, it would take about 8 oz of chocolate to be fatal, but it is still dangerous.
I think I have some idea where you are going with the Mahwee and bugs, but I haven't figured out how you are going to deal with the power loss. I would just shut down the transmitter and run a power line to the colony and then cables to the vital structures as a temporary measure, assuming of course they can scrounge up enough cable. Otherwise I would try moving the generator from the dig site to the colony and using it to power the hospital and maybe command center. Again, that assumes that there is no major issue with that.
One last nitpick, I'm a Texan, and I have to say, Trip's grammar is bad even by Texas standards. Using "were" instead of "was" in one spot is pretty atrocious. Some words that Texans do use are "Y'all" as a contraction of "you all" and can be both singular and plural, and "gonna" instead of "going to". Ex: "Y'all gonna finish that sandwich?" Another one is "doin" instead of "doing". Ex:: "what the hell are y'all doin? I'm gonna kick your ass". You can also look on youtube for Dr. Red Duke, he did a lot of health segments and is a sample of how someone can be very intelligent and talk with a thick Texas accent.
Hope that helps