Nice Job! Those are some nice batteries too! I've looked at them in the past when I was entertaining an electric conversion.
I haven't read through your build blog yet but plan to when I have some time. Since I haven't yet, would you mind sharing what voltage your primarily running the car at?
Also, going back to your original question regarding gear ratios and wanting to get a lower final drive. An Si gearbox will definitely give you a lower gear ratio than anything that came in the HFs but the HFs actually came with three different final drive ratios. Depending on where the car was originally sold in the US, 49st, Cali, and mountain regions. Obviously the most common is the 49 state models which (according to the manuals) came with a 2.95:1 FD. The other two (again, according to the manuals) were 3.55:1 and 4.06:1 respectively.
So, depending on which FD you currently have you could be looking at using significantly different gears with the Si box than you are with the HF box. I know you're not using all the gears...are you?
Again, it looks like you've done a really nice job considering where you admittedly started at. I'm impressed.
Jay