Truly MMM would be to get rid of the car / loan, ride your bike an use zipcar / etc. May or may not be an option in your area.
Still in the MMM realm would be to get rid of the car / loan, get a "good used" car for 3-4k (which is hard to find), ride your bike whenever possible.
My opinion based on owning more than 75 cars (not at once) is that trying to economize by buying a 3-4k car is a fools errand for most people. If you have no intention of doing mild to moderate car maintenance (and by moderate, I mean, timing belt changes, brakes, A/C, even a clutch), then maintaining the average 3-4k car is going to cost way more than making a payment on a car that requires little to no maintenance other than oil changes, tires, and sundry items. The Yaris is an immenently simple vehicle, with simple, proven, reliable parts. Unlikely to puke up something expensive even up to 150k miles. If you have a full life where worrying if your car is going to start is a non-starter, I wouldn't get rid of the Yaris unless you found a truly viable alternative (much cheaper even after tax / title / license, much better MPG, which I would guess even a Prius wouldn't get over a Yaris, etc.).
Assuming you keep the Yaris, the second question is the loan. From a pure economic perspective, if your investments can make more than 2.49%, it makes sense to not pay off the loan and instead invest the money. From an emotional perspective, if you see debt as a chain around your ankle, it might make sense to pay off your loan. I think it just depends on your personality and goals.