Heh....I can describe some really fun ones on this! But I have to get to work!!!
1 - Yes he can. There is NO rule about the "speed of delivery", except for a quick pitch, and that has to do with the batter being ready in the box only.
2 - No, it does not! As long as the pitcher satisfies what is required of him to pitch the ball legally, he can change the way he does his windup at will.
3 - A balk is a balk. If he balks, call it. I think you are thinking too far into this. Most coaches do!
But really, there is no such thing as a "regular pitch", thus, there is no way for a "regular pitch" to challenge a balk. There IS legal pitches, and illegal pitches. If the pitcher does an illegal pitch with runners on base, it is a balk.
Anyway, sounds like you probably got the call right. Every time this scenario has come up in a game, and the pitcher has done something different than usual from the windup, the offensive teams coach has always argued that the pitcher balked, and it was always a pretty heated discussion. Such is the life of a baseball umpire. It is an unusual play, and I am sure that more than a few umpires call it wrong.