Junk Science, here are a few friendly comments to think on.
-While you are right that you didn't get a consensus response to your question, if you read through the posts, the people who have used this type of system were in consensus agreement that it does work. I would include you in this group, since you are PR'ing. (you are always going to get people on this board who rip things...especially things that are different than they are used to. That is the nature of this board.)
-While I know there are bad coaches out there, it would appear, based on the limited info you have provided, your coach has a plan and you are PR'ing. I certainly don't endorse blindly following anyone, but the proof is in the results. The more you doubt, the less you will achieve. Be wise, but be careful in your criticism. You chose that school and I assume you chose that coach. Live with your choice and keep improving. Don't let unreasonable doubt rob you of your potential. Athlete-Coach trust is essential to success, in my opinion.
-If you don't like your training, or you have questions or doubts, ask for a sit-down meeting with your coach. Learning why things are done helps you to have more trust in him, in yourself, and allows you to learn. You should do that before you post on a message board like this where a lot of unqualified people will give you unqualified opinions.
-I would also strongly suggest you talk to your coach about which event is best for you. Asking on here will serve no purpose. An examination of your PR's on a message board doesn't tell anyone who is a legitimate expert anything about your ability. Your coach is the one who sees your workouts, understands your talents, knows your body type, knows your previous running history and hopefully knows your mental and physical limitations.
-In regards to being really tired after the second workout, that is normal, so don't worry about it. It is training, and if you are training to be fast, it is going to take a toll. There is a difference between being exhausted from training at a high level and burning out. I would say if you are feeling that way and are PR'ing, you just aren't used to training at the right level yet. You aren't going to be running PR's if you are burning out, so it would seem your body is dealing with the training fine so far. Also understand that while the consecutive two days do take a lot out of you, that is also why this style of training provides 48 hours of recovery time after the second workout. (as a side note, for what it's worth, when in the right mental state my athletes often had better practices on the second day)
-Injuries. First, for athletes training at a high level, there are going to be some injuries along the way. You said you were worried about getting injured because a teammate or teammates have been injured. You need to determine if most of the team is getting injured, how often the injuries are happening, and what type of injuries are occurring. If your team is getting stress related injuries, then there probably is a problem in the training program. In my opinion, stress fractures should be a rare to nonexistant occurance in a program. Normal little things (a case of shin splints or two, soreness, etc) or freak things (ankle sprains for example) are not usually what you look at in determining if a training plan is causing injury.
Anyway, just some comments that might help. I strongly suggest you develop your relationship with your coach though. It sounds to me like trust is the biggest issue here.
Have a great season!