For the instrument panel stiffeners, should I flox the corner where the two layups come together at 90 degrees?
No. In this case, use dry micro to form a radius to help the BID cloth to bend during the layup. Flox corners are generally used for structural joints where glass to glass bonding is required. The plans are pretty good about calling out flox corners when they are needed. If you need a radius in a corner, use micro unless told otherwise.