Originally I had a 100 amp service cutoff in the garage which fed two 100 amp (capacity) panels in the house (upstairs and downstairs). This was original to the house built in 1951. The new service created a 200 amp feed-through service in the garage, converted the downstairs panel to a 200 amp main panel, and kept the original 100 amp subpanel upstairs now as a subpanel from the downstairs panel. I know they didn't follow the NEC code in one area (junction box) so now I'm questioning the whole job...
The new upgraded configuration is as follows:
200 Amp feed-through panel in garage with 8 slots for garage stuff. A two-inch metallic conduit carries six copper wires underground (under the garage slab) to a junction box in the crawl-space of the house (two hots each 00, one neutral #2, and three bare grounds going to different locations each #6). The three bare copper wires were from the original and could not be removed when they pulled the other original wires out. Four of the wires (00, 00, 2, 6) go straight through the junction box (an original 12" junction box which is too small hence the code violation I know about) in a straight pull then proceed through two inch conduit to the main 200 amp panel downstairs. The other two #6AWG wires go to copper plumbing next to the box and the 100 amp subpanel upstairs through a two inch raceway out of the top of the box. Two hots (#4AWG) now come from the main panel downstairs and travel back through the conduit, through the junction box, and through the two inch raceway to the 100 amp subpanel upstairs (an angle pull). These #4 wires were original and used to go from the upstairs box to the garage. Two pairs of smaller wires (original) come from the upstairs subpanel and go out of the left and right sides of the junction box in conduit for the oven and another item.

First of all, are all these wire sizes OK? They told me the metallic underground is suitable for bonding as well, so they didn't need to run a second #2 ground; therefore the #6 wire is extra grounding. Second, is it OK for the subpanel wires to travel back through the same conduit to get to the junction box and then upstairs? I think this may not be allowed.
By my calculation that junction box should be at least 16" long and 12" high, but it is 12" long and 6" high. I posted a picture of the junction box seen from the bottom (see link below).
THANK YOU for helping!

How did you decide on the required volume?

Grounds only count as a single conductor of the largest size present.