Never really noticed until now as never needed it as I just use a logical form flow.

However I have created a custom form which follows a graphical workflow, and I need to alter the tab-index from a logical top->bottom

Is this possible in the JCook JDOM?

What do you mean ?

Steps for your forms, such as checkout a payement ?

I have it in my ideas lists. I did it in past.
For the moment you can use the redirections :
call yours layouts with suffix (_1, _2, _3), and then create manually all redirections
cancel > previous layout
save > next layout

Is it an answer ?

No, literally the tabindex settings that you can put on any element on a single form.

SO I have a form, and when you TAB through it, it jumps from field to field in a logical manner as no element has a tabindex defined

I have an 'illogically' laid out form that I want to jump through the fields in a different order (it makes sense when you see it) i.e

<div><input tabindex="2" value="Should be second"></div>
<div><input tabindex="1" value="Should be first"></div>
<div><input tabindex="3" value="Second be third"></div>

Hope that makes better sense

Create event 'keypress' or 'keydown', (I do not remember wich one catch the 'Tab' key.) on every concerned field.
(For that you will make a loop. Do not do that for each field manually)

Then search for the next field with a JS script research (jQuery or MooTools), and make :
and eventually then
I experienced some issues with that. And still in the new builder interface (cook), I have some fields not wanting to work because the dom is not ready or I don't know why. Anyways...