A few comments.

1. Your chain line looks ok. If you can take a pic of it in the middle front ring and middle rear cog I can get a better idea.
2. You chains too short. Look at pic #4. Lengthen the chain until it hits the upper pully wheel then remove 1 link. You want the 2 pully wheels as parralel to the ground as possible. Lengthening the chain may help alot of your shifting problems. What kind of chain is it?
3. Remove some drivside axle spacers. Get that outer cog as close to the frame as possible. This will improve RD performance. A slight re-dish of the rear wheel may be needed.
4. Did you pay your model with popsicles?