As for your strap and know issues with the head tefillin, I suggest that you make adjustments until it fits properly, with the knot at the base of the skull and the tefillah sitting just at the front of the spot on the head that is soft when a baby is born. [see Mishneh Thorah, Hilkhoth Tefillin 4:1]
If you are unable to make it work, then I would confer with a competent rabbi or scribe. If this does not work, then I would seriously consider replacing your ressu`oth with newer, more predictable straps.
One of the common problems that I see is that people do not give their tefillah shel rosh enough slack around the sides of their head because they either are wanting the bayith to sit almost directly on top of their head, or they are concerned about it sitting too close to their hairline, or both. This is especially a problem if your batim are larger. But if one gives more slack and aims to set the shel rosh more toward the front of their head, just a centimeter or so above their front hairline, then everything will sit better and will be worn more comfortably.
A more expensive option is to trade in your current tefillin for something closer to 2x2 cm in size, as made by many Temani soferim in Eress Yisra'el. Many find them to be the "Cadillac" of tefillin in both quality and comfort, and once they make the switch they rarely go back.
As for the excess straps flipping over, it is not a halakhic problem at all unless the underside is red. Otherwise, if it the usual white-gray or greenish color, it is completely fine. This is explicitly stated and explained in Mishneh Thorah, Hilkhoth Tefillin 3:14.