I actually purchased the tickets last year in august. so we will have seats i was just worried about crowding, also the CL gets in very early into TOL around 5 something and my wife would not like to get up that early or myself. We are getitng dropped off by my parents so will not have to use parking. I also just checked and CL is sold out for that day as well
With Amtrak's reservation system, train 49 and 449 are two separate trains on the computer, but in reality, they are the same. That just means the 449 section of seats has sold out, but still seats left on train 49.
As for bags, you can always check them to SFC. Sounds like you have at least 3 or more, so maybe check a couple that you won't need at all during the journey. Then you can have the others, so you have change clothes and such. I would carry on the guitar. This way, you won't have to worry about finding space for them when you board the LSL, and you won't have to bother with them during your layover in Chicago. They will be transfered for you.
You shouldn't worry about not getting seats together. Amtrak attendants try their best to keep double seats open for those passengers who get on down the line. Should you not find any, simply ask the attendant or conductor to help out and you get you together.
When I'm in a sleeper, I really enjoy a crowded train. It just seems like a big party is heading out west and you can meet lots of great people, and when you need to get away, you can escape to the privacy of your room. In the roomette, you might can keep a small bag in the room with you beside the seat or under the seats. Otherwise, there is a large luggage rack on the lower lever of the sleeping car as you board.
Hope you have a great trip!