That video Peelywally links to is very good around foot/ankle position and pedalling in circles and you're definitely going about it the right way by getting your saddle/pedal relationship sorted first.
The bars should then feed from that, in your video it looks like the bars are too close in, but this may differ a bit now as you've since adjusted the saddle again. It all gets a bit trial and error for the bars but you need to think about your weight distribution. Based on your saddle/pedal position there will be a natural angle your upper body will want to settle at, this can vary according to personal flexibility. If the bars are too close you'll be pushing your upper body back and up as it constantly tries to dip lower. You'll also be sitting heavier on the saddle than your position is suited to and, in that scenario, I'd expect to suffer from hand, wrist and butt problems with possibly some shoulder issues as well. These may be non existent on a shorter ride but as you get beyond 30-40 miles will start to make themselves felt. They can go from mildly annoying to excruciating within 2-3 miles, at least it did with me. If you look at the chart on this page:-
http://www.prodigalchild.net/Bicycle6.htm
scroll down about 1/8th of the way and it shows road bike stats based on the guys building/shop experience versus customer stats. For flat bars with bar ends I find these fit pretty well, so just have a look at your height, inseam and footsize and see what your suggested TT and stem are compared to what you have. I've followed different detailed setups and all of my bikes end up within a few mm of Daves chart.
Thankfully messing about with stems is easy, you can adjust the height by altering the spacers positon, flip the angle or try a new stem...to see what difference a stem will actually make this site is invaluable:-
http://alex.phred.org/stemchart/Default.aspx
you plug in your existing dimesnions for stem length, stem angle, HT angle and spacers and then can plug in a new set of data and see how the two positions compare.
If you get your saddle right then don't be tempted to move this rather than the bars.