char inChar=file.read(); //Get the first byte in the file.
while(inChar >0){
char inChar = file.read();
Get the first byte. If it's not NULL, throw it away. Well, OK. I guess that will work.
Define another variable named inChar, that is local to the while loop. Guess what you have now. An infinite loop. The while loop variable never changes value, so the loop never ends.
In fact my file "Test.txt" contains 3digit-numbers from 0 to 255, like this :
"076;234;145;024;245;ect..."
No <? No >? So, why are SOP and EOP defined as < and >?
char inData[1000];
Between this array and the SD library, 3/4 of your SRAM is gone.
byte index;
You can not use a byte sized index into a 1000 element array.
We are here because all pending serial data has been read , does it change something in the code ?
You'll never get there. So, don't worry about it.
Fix the issues above, then we can talk.