Despite the much poorer battery placement on the Specialized, it blows the Trek out of the water. It just depends on what's more important to you, battery placement or good suspension. I have a similar, but perhaps a year or two younger FSR, and it freaking rocks. The age of it may require you to replace both the front forks and the rear shock. A new rear shock for the FSR is a bit harder to find than others, but chain reaction cycles has it for about $100. I had to get one for mine.
The trek has a simple pivot suspension, fine in its day, but to prevent pogo you have to set it up hard as a rock. Prob how a 15 year old elastomer is anyway.
In other words, it will either bob a lot, or feel like a hardtail. The FSR however, has a very sophisticated rear suspension linkage with multiple pivot points that nearly elimiates pedal bob, even when set up very soft. You won't want it too soft, with a motor on there, but nevertheless it will really suck up the pavement cracks like they are just painted lines. Primitve suspension helps a lot, but you'll still feel every crack. Even if you don't pedal hard that much, when you need to a lot of pedal bob sucks.
Back to battery placement, if you are going to use lipo, it won't be so hard to make small boxes to strap to the frame. If you have a big headway pack, you'd HAVE to have that triangle space.
It's true though, making a torque plate for the rear drops of the trek is not going to be easy as pie. But it's a lot easier, when you buy magudamans torque plate. See the CNC thead in for sale new for a look.
It sounds like the rear shock is an elastomer of some sort. The guy did call me back so I will look at it. Says it is a 94 I think. I hope I hear back on the FSR 
The only oops I had was when after unhooking the batteries the leads to the controller touched each other causing a spark from the charged caps. No go now and it cogs if you spin the motor backwards with the controller hooked up. Any ideas what it might have fried? 
