Are there any noticable cracks inside? How about outside above the foundation crack? You mention that a crack runs down the wall between the orignal foundation and the addition. It sounds as if the foundations were not tied together properly...don't panic, go down to the local builder supply, you should be able to find some large Simpson "L" brackets for earthquake retrofit. Purchace some Epoxy and expansion bolts. Use a hammer drill to drill into the concrete, put in some epoxy and set the bolts in place, put the brackets on and tighten the bolts. 2 inside and 2 outside should do for a 2' wall
Since the house is built on clay, it will move quite a bit. Do every thing that you can to remove surface water. Put gutter downspouts into a tightline drain, do not tie them into the french drain, make sure that the ground slopes away from the house 1/2" per foot for at least 6'. If you decide to install a french drain around the house next to the foundation, dig down to the bottom of the footing, lay in some fabric weed mat in a "U" shape. Put the drain tile in and cover with washed rock. Close up the weed mat, and cover with soil. Check the yard up hill from the house, are there any wet spots?
Rent a builders level and check the addition to see if it is level. If you are +/- 1/4" you are in great shape, within +/- 1/2" OK. If it is out more than +/- 1" now you got some problems, time to call in a pro. I have seen additions out of level 3 1/2" in 30'.
The window that will not shut... check to see if it is plumb, level and square. If the addition is fairly level, just reset the window.