Electric assist is an excellent idea - an idea I am throwing around for the wife's Matrix as well.
Driving the front of the engine will work and it is the simplest, but then hybrid assist must always be linked with engine assist, aka - you cannot do EV only. Instead, I would find a way to drive one axle with the Kubota and the other with the electric motor. Either direct drive the rear axle and keep it in "4WD" (which will actually be front wheel drive) or vice versa. It all depends on space for EV parts. That way you can kill the Kubota for stop and go traffic.
I would also go with a good AC system (if the budget allows - $4600 for the AC50/Curtis) so that you have regenerative braking. That way even when you are relying on the Kubota, it will be much more efficient in city traffic.
My dilemma is that my wife's Matrix is FWD. So either I buy an AWD rear diff/suspension (it's all different) and EV the rear, or I buy an AWD transmission to drive it from the "PTO" at the back.
Or I drop $40K on a Fusion Hybrid Energi.