Hello. Compensatory services are very complicated, but I will attempt to answer each of your questions below:
1. Although you should check with your state department of education, generally, compensatory services do not have to be provided on a 1:1 basis. It depends on how much progress (or lack of progress) the child made after being denied the required services. To determine this, you may need to request an IEE to show that the child could have made more progress had the required services been given. The goal is to get the child to the point they would have been had the services been provided, but this does not necessarily mean that make-up services have to be 1:1.
2. ESY and compensatory services are two distinct services based on two distinct determinations and cannot be provided concurrently.
3. Who can be a "Reading Specialist" is likely defined by requirements set forth by your state department of education. A general education teacher may very well meet the definition depending on his/her training in early intervention reading, etc., or whatever the state requires. But if the IEP states "Reading Specialist," it has to be someone that meets this definition. I do not think a PWN would be appropriate to deny something already written into an IEP. An amendment would be the correct route, but I would fight that.
4. If they are not using Wilson and that is written into the IEP, they are in violation. I'm surprised they stated a specific methodology if they can't/won't use it. The problem you might encounter, however, if you tried to enforce this by way of a state complaint or due process is that the state or hearing officer would be sympathetic to the school district if they could show the methodology they are using is comparable to Wilson. Again, they should amend the IEP if they are not going to follow it. A PWN does not give a school district a pass on implementing what's already written into an IEP.