ok, you removed the two 5 cell assemblies in order to get access to those two terminals, the red and black shrink colored terminals? so normally the two 5 cell packs would be bolted on to those terminals?
be very careful because if you burn up something, there is no replacement from E+. so maybe take the A123 pack back off until we can identify some of the components on the pcbs and look at how the wiring is laid out.
you said DSP, do you mean a digital signal processor board? and the other board you called 'power' and so that is the real controller board that creates the phase wire currents?
each 5 cell pack has a connector to the DSP board? when you remove power from the A123 and the other 4 packs still attached then if you can take pictures of where the 5 cell packs attach to the board so we can see where the traces run and if they connect to optoisolators (so we would need to create a signal there for the opto, or a voltage source coming back up to this DSP board from the 5V regulated voltage on the power board or this DSP board) that take a digital signal to the other side of the DSP board. they would go to some processor that monitors the opto for the LVC of each section of 5S cells. those signal may be able to be replaced by a signal we could create from another set of optos that would trick the DSP into thinking the nimh cells were still working and installed and above the LVC spec since the optos would be triggered by a false signal from a 'created' source, that source could be just one source, with the 6 separate leads to the processor pins to keep it thinking the 6 packs are still there and above the LVC. that would allow you to remove the 6 packs of nimh if you wanted to. i still wonder if you cannot keep those cells there and put your lifepo4 pack in parallel, but i think you have already decided you want to remove them.
but if the nimh stayed there, the red lug is where you would put the 20V/30V diode to isolate the nimh from the lifepo4 and the lifepo4 would bolt up right there where you have the A123 now, and the power of the 48V lifepo4 would flow at the full 58V right to the controller from that terminal. but instead of allowing the last or top of the 6 5cell packs to connect directly to that red terminal. you would attach the diode cathode to the top of that last 5 cell pack and the anode of the diode would attach to the red lug. that would block regen into the nimh pack but you would still be able to get regen to the lifepo4 pack if the controller would allow it. but i am assuming the red lug goes to the controller, or power board as you call it.
just be careful now if you have it open and really worry about shorting anything right now since you cannot get parts as you know. you really are taking a big risk like ambrose said, so be careful.
you should be able to remove the other nimh packs too and take the board free so you can take better close up photos of each side, these would be worth archiving since i doubt if anyone ever gets the opportunity to see the layout of these boards again. also record all the part numbers right away too in case you burn up a part by shorting it by accident so we have a visual record of the parts and can know what to replace them with.
maybe when we look at the power board we can see what the input voltage regulation is about and how to design it to work at the higher voltage of the 48V lifepo4 pack and if there are caps that would need replacing or mosfets that would need upgrading too. you don't even have to use the full 48V lifepo4, maybe just 14S lifepo4, 51V max. i bet all the parts would still work and we could modify the BMS for 14S from a 16S BMS and adjust the lifepo4 charger to 14S lifepo4.
or you could go lipo too but you have the A123 cells. in fact you have some extras since they forced you to buy more to get the replacements. as i recall you have 5 extra, which would get you to 17S but just 16S would leave you with the regular 48V setup of 16S BMS and charger, plus a spare cell that is known good and the other three iffies that you were worried about.
this could be the fastest E+ on the planet. the diode would protect the nimh, in fact the nimh would never really provide much current, until the lifepo4 had run down to 36V itself, and then the load would be shared between the two packs after that. fast fast fast.
way cool miro. cutting edge.