Conduit fill size when using multiple cables of different sizes
Stripping the jacket off the cables is not an option. The wires inside are only rated as part of a cable assembly, and cannot be used as individual wires.

I didn't check your numbers, but the process you followed is correct. 

If you're dead set on installing cables, you might want to bump the conduit up a size. The extra space will make the pull a bit easier. Also make sure you use plenty of lube. Though since you're installing conduit anyway, consider installing individual wires instead of cables.

It also might make more sense to bump up the size of the feeder a bit, and eliminate the two branch circuits.  Increase the size of the secondary panel, and supply the 20 ampere branch circuits from there instead. This might save money on materials, make the pull easier, and reduce the size of the conduit (not sure about this, as I haven't run any numbers).