Dontheone:
My first question is what sequence does the program go through when compiling and loading the program? Does it go through each of the includes in order that they are listed in the include list or does it go through the program and go to the includes when called by the main part of the program?
The compiler does nothing with the .h files until is about to compile a .ino, .cpp, or .c file that has a "#include" line that names the .h file. Then it parses the .h file as it it were part of the code file it is compiling.
Dontheone:
Second question If a sensor is bad or missing and provides no data will a sketch continue or just stall untill repaired?
It depends on how the hardware behaves and how the code was written. It could hang, return an out-of-range value to indicate an error, or return invalid data.
Dontheone:
Any pointers or information would sure help to trouble shoot the sketch.
For now, don't worry too much about warnings. Look at every error, starting at the top. If you can figure out how to fix it, do that, but sometimes a "not defined in this scope" error means that an error further down prevented a function from compiling. After you fix each error, RE-COMPILE. No sense in trying to fix errors that were caused by cascade effects of errors that no longer exist.