Having owned my 1966 Mustang since 1990, I have a pretty good amount of experience with them, especially the sixes. Mine is a 200 ci, 3 speed as well.
It looks to be in really good shape and from the pictures the body looks straight. It will be less vluable due to the lack of a V-8 as there are a lot of small differences between the V-8 and six cars. You will only have 4 lug wheels, smaller brakes, a smaller rear end, and the main difference is the 3 speed.
I am guessing that this car is equipeed with 2.77 three speed, which did not have a synchronized 1st gear. Not too big of an issue as long as you know not to try to down shift into it. As a 17 yo I drove mine with that same transmission for years. I eventually upgraded to a 3.03 three speed out of a V-8 car.
The car does have 1965 hub caps on it, not really that big of a deal.
They are great cars to drive. I used to drive mine every year from VA to IA for college. Don't get too discouraged on the six, they came with 120 hp, so you are right, it won't blow the doors off of anything unless you do what I have done:
Feel free to message me with any questions. Oh yeah, if you to get it, make sure the battery tie down plate is not rusty or your battery could come loose and get dissected by the fan (see the hood in my above picture).
Bill