What altitude are you trying to land from? Unless something changed in 1.9.1, I haven't had any problem with landing with mechjeb. If you are too low, MJ might end up overshooting or undershooting the target. When going to Mun, I get into a 50km orbit first and then use the landing autopilot. I haven't had a miss yet. So far I've used the small 3m engine and the thrust vectoring 1m engine. My first two lander were 3m landers with the crew fuel tank and some small 1m tanks strapped to the side. Landed with plenty of fuel. My second lander was one that had already landed, I was just moving it. MechJeb almost planted it right on top of my first lander and I had to use RCS to push it to the side. If you give MJ enough room to land, it will land perfectly. Also, is there any sort of manual for the rendezvous module? I noticed the MJ manual wiki is outdated and want to know how to properly use the Smart A.S.S. to meet another craft.