The answer is really easier than one may think. The main thing to remember is that the suffixes cannot be applied across the board - rather they are unique to each vehicle model (IE A M35A3 has a Cummins and an automatic, whereas the M109A3 has a Multifuel and a manual tranny.)
As various minor changes are introduced, suffixes were added. A classic example is the "Easy Eight" Sherman of late WWII fame. The actual model number was M4A3E8.
The M4 was the basic Sherman, powered by a radial engine. The Ford GAA V-8 installation brought about the A3 suffix - the wide HVSS suspension was the eighth EXperimental sub-modification - hence E8.
In the more familiar terms - the M54 was first gas powered - a variety of alternate engines were tried - I'm on the road at the moment, so this is from memory DO NOT QUOTE the specifics - but the gist is right. The M54E5 was an experimental truck with a Mack ENDT-673 diesel engine. When adopted as standard, the EXperimental designation was dropped, and the truck became the M54A1.
Hope this makes it clear as mud!
Regards,
David