Let me shed some light on this issue since my company was the first to install the Enginer 4kw kit it a Gen 2 back in May 09.
The issues with the parallel pairs was needed to help balance the high and low cells. What I would recommend is to separate all cells before any charging and record the static charge on them. Add all voltages together and divide by the total number of cells you have. This will give you a cell average that you are looking for. I would then start matching highs and lows within the cells to match the average as close as possible. This will give you the best pairings for each parallel pair.
The reason we have to do this is because you are charging the whole pack to around 58 volts and the biggest danger to these cells is overcharging. You could have a low cell starting the charge cycle at 2.7v and a high cell at 4.1v.
If they are wired in series they will both continue to receive charge until the total system voltage is achieved. This would in our experience drive the high cell to over 5 volts and damage it before the low cell would be high enough.
Connecting these in parallel, creates a balancer for that high and low cell by using one to balance the other.
We have been fighting this battle since may and my company has been through about 3 complete sets of the batteries, while trying to get all the bugs worked out.
The ideal setup would be to have individual chargers for each cell and have a low cell monitor to shut down the dc/dc when the low cell monitor detects any cell below the preset low limit.
These features would add additional cost to the system and would end up making it unaffordable to the average enthusiast.
My company is working on some upgrades for the system to allow those with the desire to improve the basic system to do so.
We will make these available on our website soon at
Remanufactured Hybrid Vehicle Battery Packs
I will try to follow this thread and answer any other questions anyone has or please feel free to contact me directly.