Setup between bikes

^Ditto, leave your first/current bike alone (assuming it feels comfy) and measure it to get the relevant dimensions.

Set the saddle height on your new bike based on the measurements, then set your saddle fore/aft (you can measure from the nose of the saddle to the steerer tube for a rough guide) as well as saddle angle - re-adjust height if necessary.

All you then have to do is work out stem length/drop. Again, use measurements as a guide, but differing geometry may require different size stem etc. With the drop, it's best to start high, then move the stem down - you also need to consider that, when you lower your stem, it lengthens the reach by about 0.3cm per 1cm of drop (based on a head tube angle of about 73 degrees).

Also worth considering riding style, if you have one more racey bike and one more relaxed bike, you'll want slightly different riding positions.

Leave current bike alone, and use it as a reference point. Use the published stack and reach figures, and work out how much your new bike is longer/higher/shorter. That will help you calculate the length of stem you require to match the reach of your old bike, and the number of spacers under the stem to match the stack of the old bike. Then once you have the bars right, simply measure back from the front of bars to front of saddle to get the saddle-to-bars dimension right. Do all that and both bikes should feel identical. It's not hard but use measurements, not fiddling about with one bit and then another.

Crazy legs says LEAVE. YOUR CURRENT. BIKE. ALONE!

Dont adjust your first bike, take all measurements and get new bike as near as dammit in setup. Especially seat height and nose of seat to handlebar stem.  Stack you can adjust as you go along.

Quote:

I would have assumed that they should be identical but now I am bouncing between bikes finding one better than the other and adjusting it only to adjust it more then going back to the other bike and doing the same adjustments. and repeat....

LEAVE. YOUR CURRENT. BIKE. ALONE!

That (presumably) works and fits and everything is fine? Yes? If no then you've got a wider problem which you need to sort entirely separately to the new bike so if you've got joint pain, saddle sore etc, solve it on that bike first.

All done with Bike 1? Good. Now move onto Bike 2, look at it's intended purpose and then set it up accordingly. The measurements do not need to match mm for mm - in fact I'd be surprised if you could do that on two completely identical bikes without spending an awful lot of time and effort literally building both bikes from absolute scratch and then you end up with two identical bikes which is fine if you're a WorldTour rider and your mechanic is lifting the replacement down from the car and utterly useless if you're an average Joe because you've negated the whole point of N+!!

There will be subtle differences in frame angles, tyre size (and therefore absolute height off the ground), BB drop, headset stack height etc that make it near impossible to replicate the positions and you have to ask yourself if it's two different bikes why you'd want the same positon anyway.

Even on my two road bikes that I mentioned earlier. One is mine, one is on extended loan which has limited the amount of adjustment and change I can make to it (like trimming the steerer tube). My bike is quite old, the "loan" bike is much more recent so there are subtle changes to geometry - even though they're from the same manufacturer and nominally the same frame size. Both are completely comfortable.

By all means use the old bike as a guide but don't try and replicate the position.

It's to do with the geometry and intended purpose of the bike. I would never attempt to achieve the same fit on all my bikes - I've got 2 road bikes (one is mine, one is on extended loan!), a SS road bike, a CX bike, a track bike and the position on all of them is different. All of them have different saddles. The CX bike has MTB spd pedals, the rest use SPD-SL. The bars are different widths. Even the stems are different lengths and angles.

Set each bike up as comfortable for you based on it's intended purpose. If you've got a touring bike, you're not going to want the same saddle, bar height etc to your time trial bike (extreme example but you get my point).

If the seat tube angle on both bikes differ your saddle fit will be dissimliar.

For different bikes you need to be taking measurements from the ground. Go ground to top of saddle and then ground to nose of the saddle. 

Also, try measuring the centre of the bar to the floor for both bikes. Then ideally you need to go on a level measurement from the centre of the seatpost to the centre of your bars (obviously this only works if you're using the same bar reach and shifters)

As above.... setting up the bike you need to consider all three contact points. Saddle, pedals and handlebars.

So although you appear to have tried to mirror the saddle height and crank length have you considered the top tube length and stem length?

Also bear in mind that if one bike is more aggressive then it will affect the set up.

I'd venture it's going to depend on the geometry of both bikes? Are they based on the same frame?

I suspect you would find the same saddle height too high on the one with the more agressive geometry?