Sounds like an interesting idea. The Etek has been out of production for a fair while now though, so I doubt you'll find one, although the Mars Electric "clones" are pretty close to the old Etek specs (and beware, there is a fair bit of "passing off" going on with non-B&S Etek motors being badged as Eteks by some retailers).
As for batteries, you can get a lot better cells than those Polyquest ones for a fair bit less money. One or two folk on the ES forum have tested the Nano range from Hobby King and found them to be superb for very, very high rate discharge : http://www.hobbycity.com/hobbyking/stor ... rentCat=85
Take a look at this thread to see just what the Nano cells will do: http://endless-sphere.com/forums/viewto ... 14&t=22464
Pack balance won't be an issue, just balance charge periodically and the cells will stay in balance just fine. These things are a heck of a lot more robust now than they are credited with, it takes serious abuse to kill them.
I'd suggest connecting the electric motor via a one-way clutch of some sort, so that you don't waste engine power turning the motor. The contactor idea has merit because it's simple, so is worth a try. My only concern is how long the contactor would last, but then again old controllers just used banks of contactors and they lasted OK. I have a feeling that some fork lift trucks just use big contactors, too, so they might be a fruitful hunting ground for parts.
Have you looked at the bigger motor that's similar to the Etek in many ways, the Mars ME0709? (this one: http://www.marselectricllc.com/me07091.html
). It has a lower Kv, but a higher power rating than the old Etek, but it is a bit heavier. I have a new one that's spare if you're interested, complete with a new Alltrax 48V controller. Mars also make a higher Kv motor that is similar to the old Etek, the ME0708, and that is a direct replacement in terms of ratings: http://www.marselectricllc.com/me07081.html
Sounds like an interesting project.