After finally getting a chance to play ME over the past 2 days, I made some progress on my current play through.
John(didn't bother changing the name this time, just the physical aspects of the character), along with Wrex and Liara, reached Peak 15. After killing a few geth and encountering the Racni for the first time(Liara-"By the Goddess, what was that?" Wrex-"Probably just debris. Don't worry, I'll protect you." Wrex is just awesome), I fixed Mira's core. As usual, I just used omnigel. One of these days, I'll actually spend the time to figure out the puzzle's patterns in order to solve it, but I didn't have the time to do so the other night(still had 3 pages of essays to complete). After her nagging, John attended to every problem she wanted fixed. Than he reached the trams, met the ERCS mercenary captain, attended to the problems for the doctor, met Benezia, yada yada yada(all the unimportant bits), and finally encountered the Racni Queen. After considering his options and hearing Wrex and Liara bicker over the decision, he decided that she was too dangerous to live(I could have done without the overly psychotic dialogue however).
Later, he went to the Citadel to acquire some supplies. He politely told Rear Admiral Mikhailovich to go to hell, told Khalisah al-Jilani to f*** off, and met Talitha. He did his best to calm her down, but decided to forcibly inject the sedative. After seeing Corporal Toombs off himself, he could not bear the thought of seeing her do the same, and he didn't trust her to take the sedative herself. Yet helping her helped him make some form of peace within himself concerning the events at Mindoir. While on the Citadel, I completed almost every side quest(still decided against being a dick to Shaira in order to do the dirty deed), but I still need to meet Conrad 2 more times and the Salarian outside of Flux.
Afterwards, I played BDtS for the first time. When John heard Balak's second in command say he was only there to acquire slaves, he offed him. He also decided against letting Balak walk, but the death of Kate Bowman weighed heavily on him. He shot Balak multiple times and gave him to the Alliance so they could interrogate him.
Now I'm just doing some other sidequests before I head to Virmire.