Just for the record you can mount two 12 v batteries on the firewall - Ralph Love's Pink Panther has them that way and there is room to work around.  So if you really want them there, fear not it can be done.  I, and I think most builders, are putting them behind the seats in the baggage compartment with the  hydraulic pump.  This arrangement seems to work out well.

As for the rudder pedals, you might consider the "FG" rudder pedals.  You'll save some weight, complexity ( don't need second set of cables) and cost is less.  The downside is obviously, they are not adjustable in flight, but for me at least this was acceptable.  You might also take a look at Valin Thorn's pedals.  Starting over, that is probably where I would have gone. 
http://www.starflight.aero/legacy/

Dan Ballin
Leg #286