For C1 - Sub-Plus - that is for each time I take the Sub die action (not sub scoring) making it 1 point instead of zero each time i do the sub cross out action?
That is correct. The rules are saying "for each Submarine action you take"
For E2 - Flexi-Level is it just for that column or all lab tiles you no longer have to worry about black die number?
It is for all following lab tiles. That is quite clear in the german rules
For I1 Super Level - Can you jump a token from not one the board or a 0 to level 2?
A jump from level 0 to 2 is allowed in any one lab column.
For I2 Super-Copy - can you copy a score ability that doesn't have a marker on it?
One last question - When I cross-out a submarine, I can still cross-out a color bot section attached to it, correct. So if I have a white sub crossed out, I can still cross out white bots on later turns?