I've learned to not change anything unless there is a problem, and only change one thing at a time - ride on it for long enough to definitely say yay or nay - and keep working towards that perfect feel. I been at this process for 2 months on my new bike and I'd say now I'm finally getting into a 100% painfree and powerful position... a pro fit might have accomplished this in 20 minutes.

Screwin with the seat can totally change the pedaling feel - this could be desirable or not - I'd get that setup first and then tackle the handlebar placement... but really its an integrated system that all has fall together just right... when "feel" is part of the equation math becomes less of a concern and then its really just up to you to change stuff until its right.