I don't think the alignment is that difficult of an issue, but if you're really worried about it, why don't you download the free version of eagle PCB and then get the gumstix eagle libraries here:
Those include an overo part which is both J1 and J4 properly spaced and the alignment holes that will make your connectors mount properly.  You can only make 4" x 6" two layer boards with the free version of Eagle, but for as little as you want to pin out that shouldn't be an issue.

On Mon, Jun 4, 2012 at 1:46 AM, Steffen Schuetz <schuetz@cs.uni-kl.de> wrote:
as I already mentioned in another thread, I would like to use the GPMC
to communicate with an FPGA. To see if the setup in the gumstix is
producing the desired output, I would like to build a minimal expansion
board that allows me to access the GPMC signals. Therefore I would like
to know if it is possible to only use J4?
I would connect

    Pin 1 and 2     to VCC
    Pin 3 and 33   to GND

and route out the GPMC related Pins to connect to the oscilloscope. Will
that be enough to get the overo up and running and communicate to it via
the wireless interface? Or are any signals of J1 needed? By just using
one I could avoid the alignment issue...

Thanks in advance!

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