And I apologize to all for not posting the code but the reason is that code is almost 30k lines with more than 34 sub sections. It was impossible to post all of that here and I am safe to presume that no body has time to examine the cross references in the code.
This is absolutely a lame excuse! You should make the codes available in an attached file. We want to check if something has gone in your program that has accidentally written into the CLKPR Register. This is the very good possibility for the speed of the MEGA to go down.
Which "nonexistent" registers, exactly? Post the EEPROM write code that causes the problem.
You have also disregarded the request of Post#6!