the old pro way of setting up a bike was as follows---
sit on the bike in your bare feet and then with your heal on the back of the pedal adjust the saddle height till your leg is straight, then sitting upright back pedal and the only parts that should move are your legs not you waist side to side. then make sure that the saddle is level with the ground and the front of the saddle is 1 3/4 inches behind the centre of the bottom bracket, recheck the saddle height if you have moved the saddle in the last operation. the stem length is decided by putting your elbow on the front of the saddle and stretching the fingers out the stem should be 1 inch further away.
Top of the bars are usually 1 1/2 to 2 inches below the saddle height.
Make sure your shoe plates are set so that ball of your foot is in the centre of the pedal. with your leg at 90 deg sat in the saddle and the pedal at 9pm the centre of your knee should be in line with the centre of the pedal, you might then have to move the saddle backwards or forwards to get the perfect fit.
Then its a case of minor adjustments, just a word of warning, have been racing for 50 years and am still moving my saddle and bars !!!!!!
If you ever watch 'A sunday in Hell' movie see how many times Eddy Merxck adjusts his saddle before he even gets to the start !!!!
Sorry for the late reply i,ve just ot back from a week away mtb'ing in Portugal
, I'm a little confused by the seat position in regard to the bottom bracket
Going to have another setting up session over the weekend to see if I get a different feel from the bike but as I keep saying now i've seen the picture of me on it in my opinion is that I just look too big for the bike so a 57 ish frame is needed if anyone has 1 going begging