Following your shifting gears (what gears, it's electric, we don't need no stinkin gears)
I don't think you'd need anyone else's controller. The controller fitted to mine is an off the shelf Alltrax AXE4855 R5. Translation: it's a fully progammable 48 volt (nominal) that can produce 500 amps designed for series wound motors contained in a large (8.5 inch) heatsink box.
http://www.alltraxinc.com/Products_AXE.html You can get software to program this type of controller,
http://www.alltraxinc.com/Products_ControllerPro.htmlI don't know what drives the dash, so that might need to be replaced by something else (there are a couple of things on the market). I don't know how the fan is turned on and off or the power shut down if it overheats.
The charger is off the shelf with an OEM program
http://www.delta-q.com/products/quiq.shtml. It doesn't appear that they allow user reprogramming but they do say that field service staff can reprogram them to suit different chemistries.
The mounts for the agni motors seem to be all the same as near as I can tell from their website, so it should be quite possible to swap to a different one. Zero says that the motor comes to them tapped with imperial threads, but the agni website says they're tapped with M8. So you might need different bolts. The 119R motor should fit (I think) which would allow a higher rpm.
http://www.agnimotors.com/home/index.php?option=com_content&task=view&id=5&Itemid=60 You could also run a higher voltage (good if you're running R series motors that can spin faster) but that would mean a different controller and battery pack. Zilla's aren't made anymore but are too big and aren't weather proof anyway.
The battery pack would need to be restuffed with batteries (even if you don't change the voltage the pack will wear out). You can buy the molicel batteries but they are only rated for 300 charge discharge cycles by molicel (Zero seem to rate them for far far more but haven't explained the reasoning behind that). I spoke to this guy
http://www.lightningev.comuf.com/ and he thinks he can restuff the pack with A123 cells that are rated for 1000-6000 cycles for about the same cost as a new Zero pack (and it should last 3-18 times longer) however the energy density is lower and so unless you put in more cells (where?) the range would be lower. It would also probably not play nicely with the existing software.