BTB made all those plug-ins specifically to go together, however, "go together", is pretty subjective. Not everyone's views on what's "balanced" are exactly the same.
What should matter most is what
you are
happy with. If you're enjoying the game, then balance is irrelevant.
Something else to consider, and this is by no means me ragging on BTB: By his own admission, as this is the only way that I would know this, out of all the dedicated modders out there, BTB probably has the least amount of experience actually playing the game. I think one time he mentioned that he's never gotten much further than giving the ring to Fargoth. I could be mistaken though, don't quote me on that.
Of course, he's achieved much through his mods in spite of that, as plenty of people still use them.
I'd suggest taking a look through the Tweaks and Birthsigns sections of PES, see what catches your eye there. As a start, at least. Pick little things up bit by bit, steadily piecing together a more enjoyable game. It's what I do, and I credit my ability to still love Morrowind to that tactic.