Couple things:
Unc, here's a chart to give you a visual of the half life of testosterone. Basically shows that an every two week protocol puts you on a hormonal roller coaster ride:
When it comes to Clomid for TRT, it's not really that uncommone. Especially for those who desire to maintain fertility. That said, I know no one who lasted to long on it. The long term benefits just don't seem to be there.
Re clomid and estrogen, it can raise estrogen levels in some men. Think about it, if your test rises so does your estrogen. Clomid works by blocking the estrogen receptor in your hypothalamus causing it to ramp up GnRH production which signals your pituitary to ramp up production which goes downstream to your testicals for the end result, more testosterone. Clomid is both an estrogen antagonist in your brain and an agonist in your liver.