Personally tho I would use UltraStik's instead of 49-ways as you can achieve all the same plus true analog.
They look like great sticks and a lot of people seem to use them, but rotary is a must have and for me and there's no practical to do it with an Ultrastik.
your buttons are crooked, you need 4 pinball buttons (left/right flipper, left/right nudge) , and I dunno how well the spinners will work in that general vicinity. 2 GGG spinners and wheels? you must be loaded
yeah the button layout is a little weird make sense to me but will probably be mofied to suit in the final product. Good point on the pinball buttons, they were a bit of an after thought and not well thought out it seams, I'll have to see if I have enough spare inputs to add to more. No I'm not loaded, I just like to things once and doing them right.
the spinners may get in the way of the 3rd and 6th buttons.
Also the buttons that you would want to use for the spinner are on the wrong side (assuming your used to stick on left, and buttons on right)
And I strongly recommend buying some cheap wood and trying your ideas out. (you can also do it with cardboard but you can't test it too thurough.) But partical board 4x8 sheet is about 4 bucks... try out your ideas for a few days and then cut the good stuff. I say this because I've redone my 2player fighting control panel like 5 times...and I don't have all the items on it you do 
Yeah the placement of the spinner worries me a little, but until I have them in hand it's hard to calculate clearances, but it seam like the best place to put them to allow me to you them as steering wheels, without getting to much in the way of anything else. I probably do as you say and mock up a few designs once I've got ever thing in hand and see what works, I'm not that big on fighters so if the spinner is a little close it may now bother me that much, most of the games I'm big on a 2 or 3 button games. Make everything fit is going to be the biggest challange I thing, that why I'm thing of using the Microsoft trackball hack to save space mid control panel.
I would those buttons away from the front of the trackball.
You will hit them during GT or bowling games.
I have an exit key up there on mine. It sucks when I am having a good round of golf, then I exit out.
yeah seen a couple of people say you need to keep everything above the trackball clear, I haven't played any trackball games in the arcade so I not sure what it's like, but I may move the coin up and player start buttons to the top corners of the control panel and leave the center empty, of course then I have to work out where to put the admin buttons.
I have never seen 6 buttons in that layout before. I would recommend having the top red/yellow buttons line up with the bottom red/yellow buttons ....... basically, do not have the top red/yellow buttons shifted over like that.
Yeah it's a weard idea, I've never liked the feel of the stacked row buttons in the arcade, this layout seamed logical to me as it's like the offset in the rows of keys on a keyboard, it's basically a 4 button kink down setup (3 fingers and a thumb layout) with two extra buttons tucked underneith to the right, if that make any sense.
LeedsFan (to much to quote) but I like the look of your player button layout, it might work for me, I may grab a couple of extra push buttons so I can try a 7 button layout both standard and your sytle it may work better than the off set 6 button layout I came up with.
As for the spinners I had a single spinner mount near the top center of the control panel on my orginal design, but with the small install size of the Turbo Twists and the option of the mini racer wheels, I decided I had to have a setup that let me use the spinners for racing games as well. The fact that this puts the buttons to the left will is unlike to bother me. (but see where your coming from about only needing one spinner, but I what to me able to play two player on as many games as possible.)
From your sketch, it looks as though your design wouldn't be quite deep enough to accomodate 49-way's with a rotary hack. If you decide to go that route, check out fl0yd's page: rotary rotarytech
The 'rotary click per click in game' problem you were referring to seems to have some solutions now.
There was a timing issue with the Ultimarc rotary interface that seems to be fixed with a new chip. There's a thread or two on this you can find with a search.
Groovygamegear has a rotary interface that has (IIRC) adjustable timings. Also, replacement 49-way grommets if you have a 'squishy' 49-way that gives you problems returning to centre.
Yeah your right, I'll need to make the control panel a lot deeper to house the rotary set, the layout has been re draw dozens of time it started out with a couple of 8 way Supers, and I've never adjusted the depth. I have to have another look to see if I can find one of those threads, I did a number of searchs on rotary 49ways and optical rotaries, but few say on track for long and after reading two dozen dead end threads I gave up and start this thread.
Yeah I was plain on getting the GGG 49way Gromments to help with the joystick feel, I was also looking in using there laser cut optical encoder wheels for the Rotary assembly to improve preformance. I like the idea of the clicks that the mechanical setup would give, but I also like the idea of being able to set the rotary sensativaty so the a 1/4 turn gives a 180deg sweep in game, which just would work well with the mechanical setup as far as I can tell.
If anyone knows any do's and dont's about the GGG interfaces I be interested to know them.