Thanks Bob I appreciate the advice. Just a few point of interest.
1. The shop told me that they need to put the car on the suspension and with the motor in the car before they can do any body work because if they don't it could cause problems with alignment of the fenders etc. (It seems that this is how they like to do it) and they like to do body work this way. As you can see my car needs virtually no body work other than panel fitment.
2. Makes sense to me to go through this process on full frame and unibody cars that are being mated to a body as things do shift and end up out of alignment etc
3.I just want to make sure that before I go to meet with the body shop that I have advice from the experts and guys who do this all the time, since myself nor the shop have a lot of experience restoring Mustangs to this level
4. Just to back track and recap I originally brought the car into thew shop to just paint the engine bay. It was a roller. They did paint the engine bay and dash and cleaned up the underside of the car. Once I got the car back to my shop I put the car on the body cart and decided to send the car back to the shop so that they could clean up inside the trunk and do some paint touch ups etc.
5. After the trunk the next step was to wet sand and polish the car. I was then told that that would be a problem as there were small pinholes in the paint most likely caused by moisture in the air lines.
6. Then I decided that we would paint the car since it was already stripped and the car appeared to be in great shape. Then I was told the same thing again about the tiny bubbles and there could be adhesion issues. I then asked how much more to strip the car to bare metal. Then we proceeded to strip the car. On one hand I am ok with that since I know know what a great car I have and how rust free and clean the body is. Before that I was just assuming, albeit a very time consuming and expensive experiment indeed
7. So after all this I find myself at the point of having wasted money on bad decisions and would really like to stop the bleeding and get the car finished correctly and to the high quality I expect. While I can appreciate that the shop means well by making the car a roller, I just don't see the point if the car can be painted and mocked up while it is on the cart. Ultimately I am looking to maximize my investment and spend wisely and only when and where required. Sorry fo all this backstory, but thought some perspective may make giving advice easier if you had the full story that has been unfolding over the past year.
Photos of the car before I brought it into the shop for reference