That tiny black thing is your starter solenoid trigger? Seems kinda small, at least compared to mine. Or am I looking at the wrong wire? Post a pic of the way you have it installed now.
And no, you didn't damage you glowplugs. When the starter accidentally cranked it was just the starter cause of the misplaced trigger for it - your ignition was never on so the glowplugs controller never powered up their own relay. Assuming plugs are not on a manual switch to begin with, in which case the only way to engage them is thru said switch. So you're fine, nothing to worry about there.
The GV stuff coming alive faster is direct result of your new cables. That's why I insisted that you connect the black 4gauge cables to the battery directly, instead of copying the factory daisy chain setup. Now everything that needs power can receive as much of it as it wants, no robbing one another off it. With the factory setup you had I bet the glowplugs were hogging power from the starter relay, and since starter relay also acts as a junction for all the truck's 12V needs everything else got affected as well. That's why you see so many cables on my positive terminal, so everything can pull what it needs when it needs it without affecting anything else.
The grounds, the passenger side cable is attached to block with the same bolt that holds the metal bracket for your positive cable. Or at least that's how it was from the factory - fairly easy to replace. Driver side negative cable looks like it's bolted to the block somewhere near the water pump neck for the lower radiator hose, power steering pump hides it quite well from above but IIRC it's easily visible from under the truck. If you don't wanna mess with them just buy two more of those black 4gauge cables and add them too the negative terminals (in the same manner as you did with the positives, using the pinch bolt) then run them to convenient places on top of the engine, for example the alternator's top bolt (use a longer bolt, attach cable on back side of alternator's ear with a nut after alternator has been tightened in place) and one of the A/C compressor's mounting bolts. Also I'd recommend if possible you get the new cables in red and swap them with the black ones you already have - personally I like red for positive and black for negative, it just makes things harder to screw up accidentally next time you have to work on them.
Your secondary relay on the fender is likely for charging a coach battery on a trailer or camper. Pretty good setup actually.