I think the longer stem might help out the twitchy issue. I am not as tall as you, but suffer some of the same fit issues that all tall guys face. The bike may be twitchy because your center of gravity is favoring the rear of the bike too much. A longer stem might bring your head and shoulders a little more forward. I am 6'4" tall, long torso/arms short legs and ride a 59 c-c frame with a 72.5 deg seat tube angle, seat all the way back on a seatpost with a lot of offset. I also ride a 150 mm stem (MTB stem filed out for 26.0 bars).

I am not sure what to say about the muscle fatigue in your lower legs. Are you 'ankling' alot when you pedal? My feet stay almost dead level around the whole pedal stroke. I know a lot of people ride toes-down for part of the stroke and that could be the difference. Try to pedal circles without changing foot angle much. That may bring your quads and butt into play more...