87 745t.

Since I put the motor in car has had a very subtly rough idle, very intermittent miss. I believe I also feel, at part throttle acceleration, a split second hesitation, it isn't a cut-out at all, it's very very subtle.

I could write a small book on all the things I've checked and replaced, I wanted to relay one specific thing and get some feedback on it.
The aux electric fan, that is controlled by the thermo switch on the radiator, when it kicks on, which is seldom, the miss at idle becomes MUCH more noticeable, and the idle bumps up a few hundred RPM. Fan seems fine, I've done no diagnosis as of yet. It has to be significant though. Only other directly related, maybe, thing is that the heater blower when in position 2 or higher, when turned to 0 the idle speed goes up for a second or two then settles back in.

Thoughts?