So if anyone else has problems of Polygons faces turning invisible when extruding or adjusting shapes and un sure on how to fix it, Edit > Delete by type > History, Display > Polygons > Backculling (to turn backculling off), File > Save (or save as a new file), Restart Maya, test extrusion tools etc. then Display > Polygons > Backculling (to turn it back on) and save again.
This seems to be rare but very difficult problem to solve for newcomers (such as myself) hopefully the solution above solves this problem/bug once and for all!
With that problem solved I feel I'm going to leave my model for tonight as it's tried my patience enough for tonight. There have been so many little problems with this model so far that has escalated to larger ones that it's felt like trying to win that weird space chess game C-3PO and Chewbacca play in Star Wars, but I didn't let the Wookie that is MAYA win, and neither should you!
Modeling continues tomorrow!