Sounds like you're doing things the way we did it 20 years ago. That was fine then, but time changes and we have wonderful new parts that have internal flash and ram so we don't need all this external stuff. Apart from this, they're also much faster and got more features. They also have easier means of downloading the code and better debug features. Look at something like the Silabs product.

As to why you want/need to stop/start the crystal oscillator is beyond me. Keeping the device in reset usually stops anything else happening.

also to be technically correct - you can't program ROM - I dare say you mean EPROM.