Since flux is at a max, so should EMF. I am just not sure about whether or not this theory is right though.
In fact the opposite is true. When flux is max or min the emf is 0 and when flux is 0 the emf is at it's max or min. In order to explain why I could use calculus(maths methods will suffice) but I don't know if you do the subject so I'll try not to. Say flux is at a max when

. When

the flux is just below maximum (where

is a small duration of time). When

(just before flux being maximum) the flux is also just below max. In fact if we compute the average emf between

and

:
)-BAcos(\omega (-\delta t))}{2\delta t})
Using the fact that
=cos(-x))
the expression evaluates to

.
Play around with the formula

by computing changes in flux over littile time intervals and see how the emf varies.
As for the signs, it's all about the direction given by lenz's law. In this case the current is in one direction since every half turn the ends of the coil swap with each other and hence are touching the different part of the commutator, and this cancels out the natural change in direction that occurs every half turn in the coil(you can check this by using the

and lenze's law

.
Feel free to ask for clarifications.