You have already received some good advice, but here is some more...
1.) Paint: I used MM Acryl U.S. Army/Marines desert sand. It came out a little on the thick side (my fault) but also seems a bit on the dark side compared to photos I've seen. Should I be mixing it with white and about what ratio for a good scale effect?
The U.S. Army/Marines Desert Sand color is not a US Federal Standard (FS) paint color. It is based on a paint that was hastily bought in Saudi Arabia during the build-up to Operation Desert Storm (ODS, '90-'91) to quickly repaint NATO camo vehicles from Europe and the US as they came into theater. As stated above, Testors Model Master Sand (FS 33531) is an almost perfect match for modern CARC Tan as seen on current vehicles.
2.) I found it hard to get the tracks in place even without the side armor attached. Would it be better to assemble the upper hull seperate from the lower and join them permanently post painting?
I don't generally have an issue with tracks, esp. those that go behind skirts. The easiest way to attch them is to leave them apart until you are ready to attach them. Feed one end of the tracks through the sprocket and around the road wheels, then attach the two ends of the track. Once attached, simply rotate them so the connection point is hidden behind the skirts on the top of the road wheels.
3.) The hatches were glued in place but the hinge still works, however the paint glued them in place at the closed position. Should hatches be painted seperate and assembled later?
You can do that, but usually, properly thinned paint will not "glue" them in place and they will still be movable after painting.
4.) I used an acrylic wash of red brown which stained the underlying paint and began to lift it off. Should there be a barrier coat between base and wash? Also what is the proper wash color and is oil/enamel better than acrylic for washes?
Yes, if you are using acrylic paints, you have to seal the base coat before weathering washes and successive coats are added. A dark brown is usally a good wash color for sand vehicles and an alomost black for darker vehicles. I use enamels for the base coats and usually use acrylics for washes and weathering. I also weather after applying decals and sealing them on, see no.5.
5.) Decals pre or post weathering?
I always add them before weathering so they weather the same as the rest of the vehicle. Nothing looks worse to me than a nicely weathered vehicle with clean markings. It just doesn't make sense to see them that way.
6.) what is the best way to paint the black tires? I heard a U.S. dime is the right size to lay over the tan portion then the wheels can be airbrushed. Does that work?
I use a circle template. It is an artist's tool with a bunch of pre-cut circles of different diameters cut into it. Paint the whole roadwheel flat black, then use the circle template to match the diameter of the metal wheel center and use it to mask off the rubber part and spray the center wheel color through it. This is quick and easy. Works great every time.
Good luck with the rest of it.