Hey Mike,
I don't know how many people they will accept from the interview. As for midwestern, that is one of the two or three top DO schools in the country, so a linkage there is an awesome opportunity. Then again, UCSD has a linkage with Western, which is probably the best DO school. They don't accept everyone - this year three people applied and all three were accepted, but if more applied I think they were going to cap the number of accepted students from UCSD to about 3.
I think all three programs will be rigorous. Was the 3.4 from your postbac your best work/effort? If so, I would consider Midwestern if their linkage is for everyone. At UCSD, a 3.5 is expected to get a committee letter, and everyone has higher than that - most of us have a 4.0. Getting lower than that won't impress med schools. But, UCSD postbac offers free tutoring and tons of educational support if you're struggling in a class. Think carefully about your ability to get around a 4.0 before making a decision.
I was also concerned about the extension and big lecture aspect of UCSD. Being an extension student doesn't feel any different than being a regular undergrad. Two of your three classes each quarter will be with undergrads. I did really well in undergrad in a few of the classes they automatically enroll us in, so I have taken one alternative each quarter. That is a little stressful because we're not guaranteed a spot in an alternative class, but this quarter is the first that I haven't gotten into my first choice class. The class I did get into (Biology of Cancer) is actually awesome, and was my third choice anyway. The extension people work realllyyyyyy hard to get us enrolled, and we don't have to lift a finger, which is nice. IMO, affecting your undergrad GPA is really important - med schools look at that number immediately and it's important that it looks good enough that they don't set you aside before even realizing you did a postbac. Also, we all sit together in the undergrad classes, so it doesn't feel like you're lost in the crowd. We are also really proactive students, so we tend to go to office hours often and get to know the professors. That makes the class feel much smaller as well.
The third class you will take each quarter is just for the postbacs, taught by an amazing teacher named Steve. He does educational support for the med students - basically he knows everything they learn in medical school so he can help them, which means awesome info and opportunities to occasionally attend lectures at the med school for us! His class is very similar to first year medical school classes - pathophysiology of really common and interesting diseases, pharmacology, etc.
I think the master's thing is a non-issue. You're going to go to medical school - assuming your MCAT turns out well, I'd imagine you will at least get into a DO. Why would we need a master's?
It's a hard decision. Personally, I love UCSD. I'm thriving from feeding off the motivation of my friends in the cohort, the support from my advisor (who sits on the UCSD SoM admissions committee) and Steve. I'm really happy with my decision to go here. Seven people from last year's cohort (of I think around 23?) have been accepted to UCSD Med. Many of the other students are getting their acceptances to MDs around the country too. Their success tells me that med schools respect UCSD postbac.