Questions I have are:
1. Is the #1 AWG wire I have specified between the generator and the transfer switch support the 100 AMPs? Could I use smaller? Can I use Aluminum or does it need to be Copper?
You can use either. Copper is more expensive. If you use alum, you need bigger sizes. #1 cu would be 2/0 alum. Always use THHN rated wire and the 75 degree ratings when you figure this stuff. #1 is big. #2 would be better for your run length and that's if the breaker on the generator is 100 amps.
Here's a link for basic wire amperage vs size.
If your service is 150 amps, then the whole house switch needs to be 150 or larger. If it's the EZ switch, then it's limited circuits and the size is your choice depending on how many circuits you want to carry over.
You should make sure the breaker on the generator is 100 amps. That sounds too big for a 12KW. 20KW's have a 100 amp. My 17 KW has a 65 and smaller gens typically ave 50 amp breakers. Don't confuse the gen breaker with the transfer switch size. They're two different things. Size your wire (from gen to xfer switch) to the breaker on the generator, not the transfer switch amps.
2. Do the conduit sizes I have listed here suffice for the power and control wires or am I oversized? I am planning to use PVC for the conduit
Type "conduit fill calculator" on the internet and you'll find some easy answers for sizing conduit. For example your power conduit from gen to xfer switch can be 1 1/4 for 4 #6's. You can use 1/2 inch for your control wires.
Here's an easy one to use http://www.electrician2.com/calculat...alculator.html
3. Is there any way to tell the size of the existing SEU cable currently in use?The jacket of the cable does not appear to be marked, so the 2/0 I have listed is an assumption based on the size of the wire and the fact that it currently supports 150 amp service.
If it's alum (and I think most SEU and SER is) it's probably 3/0 or 4/0 to handle 150 amps.