I've spent a lot of time recently thinking about flux, current, induced voltages etc. I think a lot of my confusion came from not realising what has come first.
For example, current and magnetic flux are intrinsically linked, one directly creates the other. As current increases, so does flux, in phase. However, if flux creates current, the current will be 90 degrees out (assuming a power factor of 1). This is because only a changing flux will generate voltage, therefore the voltage is 90 degrees out, and therefore also the resultant current from that voltage will be 90 degrees out from the original flux.
I hope this helps. I appreciate the question is old!