My experience with mounting CRT's still in their cases is to use a wooden shelf, like you were trying. One of the things that you may learn the hard way in this hobby is to measure parts you want to use in said arcade machine before building said arcade machine. This way you can identify if the TV you want to use is too deep for the cabinet you've built. You can decase the TV but the back part of the TV is typically pretty deep too so you may not gain the clearance you need. Also, be very careful when decasing. Do a quick search on the forums to understand how to decase properly. The electrical components on the back of the TV if handled improperly/touched can kill you. Not to make you paranoid but you should handle it with care.
What you may have to do is build your shelf at the right angle, and then mount the TV in the cabinet. Then trace around where the TV comes in contact with the back part of the cab and then use a jig saw or dremmel/rotozip to cut out that part so the TV fits into the cabinet. Most people have their cabinets backed up to a wall so odds are you won't notice the TV sticking out the back. Also, this is your first from scratch cab so mistakes happen. Don't worry about it and just keep trucking along.
The part you made for the front of the TV is called a bezel (if I'm reading you right). If it doesn't fit, make a new one after the TV is successfully mounted into the cab. Once the TV is i the cab and good to go, measure the new bezel and build away.
As far as the CP sitting low, you can always add more wood like a shelf across it or if you're feeling adventurous you can always make a new CP.
All of these problems can be fixed and your machine will look great at the end of the day but if you're a perfectionist, then you might need to start over with a design built for the specific components you're using.