So I've been taking Krav for a while now, and I like it. Mainly because it's purely focused on practical self defense, which is what I want.

However, my University's winter break is ending in a couple of weeks, and there's no place in my college town that does Krav. So I've been looking at Karate or Brazilian Jiu Jitsu (the only two other than TKD offered within travel distance).

The issue is that I only want to develop muscle memory/instinct for RL scenarios. While some of the the techniques in said MAs may be practical, from what I can tell there'd be many that I've have to learn instinctively in order to advance in said MA.

For those of you who practice multiple MAs, how do you balance which techniques you use in a given scenario (ie: intense sparing)?

So if I'm understanding you correctly the question is not about which style to pick but, which school will let you train in the more productive manner(for you). As Matt has alluded to, you have to train specifically for what you want to learn. The only approach really is to know what you want going in and explain your goals to the instructor(s) and see if they are understanding.
I'm sympathetic man! I know it's hard to try to fit what you are used to into someone else's curriculum. You can always look into starting a club at school. At least you would have some sparring partners!