I cant speak directly to the grinding issues, but first thought would be misalignment of some kind. Maybe (and this is just a wild maybe here), loosening the bolts that hold starter on and wiggling it around a little might let it find slightly different position? Shot in the dark, but doesn't cost anything but a little time. If you have starter off again, wouldn't hurt to look in hole, look at teeth on ring gear, make sure they look ok / not all chewed up.
I haven't pulled one of these starters, so i'm just guessing here, but maybe starter is too deep in hole, maybe slightly shimming it out (forward) would help? I'd take it easy, do like .... 1/16" something small (and shim all the bolts holding it on equal amount, try to keep things parallel). But if you had a tiny interference issue could make a ton of noise, only take small change to make big difference. Have no idea if this is actually good idea, just throwing it out there...
If you had current starter out, it would be good to carefully compare that one with the old one after its rebuilt, carefully look at the nose section, see if you can see any differences in depth, positioning.... mainly on the gear, its shaft, etc. I'm betting rebuilding process is mostly on electrical side (like rewinding), probably not making material changes to the positioning of the critical components
On a really out there note, I wonder if something fell down inside bellhousing? small nut or bolt? Pretty random, but its always possible theres some small piece of foreign material in there where it shouldn't be, rubbing where it shouldn't be. Probably not, it would be way down on my list of items.... but i've seen crazier things.
The big wires on starter, if you keep having troubles, I'd carefully inspect them. I'm just replacing mine out of caution. They had a bunch of damage that couldn't really be seen very well until they had at least the front 3 or 4 feet pulled out. They had obviously gotten toasty at some point.... I notice my truck has newer starter on it (truck is 2003, starter is marked 2005, and starter motor outside condition looks a lot different then rest of truck too). I suspect that the fried wires and replaced starter are related. Maybe original starter had the solenoid lock closed, turn "on" and not release. Or something happened to make a dead short, for a short period of time at least. Maybe someone working on, and a wrench / tool just happened to hit both terminals at same time, make short for a few seconds? Things like that happen....
I pulled both of the big wires out of my truck, wanted to inspect whole length AND make sure they hadn't damaged anything around them. And was planning on replacing them anyways, so had to have all the way out. I did find a few things that were routed alongside them that got a little damage, mainly just some air lines, but nothing electrical except a small ding in a ground line from starter to frame rail (theres another ground line, maybe 1/0, that goes from starter ground bolt to frame rail, under starter... that one is worth checking out for you)
Once i got the big wires out, I found the damage on them was limited to fairly short section (maybe foot, foot and a half), and didn't do anything terminal to what was around it.... but had to get them out to really look at them / really look at the stuff they travel along with
If I needed to, I could have just added some insulation to mine, called it good, and it would PROBABLY be fine, but I'm replacing anyways. Burnt insulation opened up, never know how much water / corrosion could be inside rest of insulation. Or, maybe theres a break in there somewhere, that can cause huge spike in heat as current has to go through much smaller wire where break is.
One thing that concerned me with mine is, having damage inside cable I couldn't see. Its possible for a connector to get hot, kinda burn the wire inside, never make great contact again. Or, have some issue with the connector / wire connection that reduced current flow/increased resistance / increased heat.
Blah blah blah, i'm just replacing the cables and connectors (just talking about the big positive and negative cable I mentioned above) "out of an abundance of caution" I know if I dont, I'll always wonder if there is issue.... and I just dont like to have to worry / wonder about things. Its worth it to me to not have to think about it.
As a sidenote, when I was trying to get my truck to start (after I started having crank no start issues, I never looked at this before), I was able to do a cranking RPM test, and it showed the RPM as being a little low (190 to 210 rpm), they say the C12 ECM needs to see 250 rpm before it will fire injectors, so thats part of why i started digging into the starter wiring.... and why i decided to replace those damaged cables, just in case they were causing extra resistance / not flowing as much current as they should. Been going through truck and just trying to check & clean all relevant electrical connections....(making sure to hit all the ground wires)... make sure they aren't covered in corrosion, not loose, not damaged, etc. Just good long term maintenance in general, plus once you start having issues, never know if one bad terminal / connection somewhere is driving a bunch of issues. it certainly happens!! Hell, I've fixed a LOT of wiring issues on commercial trucks just by going through the wiring and looking for stuff that is obviously damaged... and fixing those damaged areas / parts. Or just cleaning, tightening connections.
Oh, as a sidenote, I pulled my dash, and found some connections there that had some corrosion on them. My truck was sold w cab armor stripped (no doors, roof, etc) I dont know how long it was left sitting w no top... but it shows plenty of sun damage, some water damage on and under dash. Not terrible, but its there. Also, dont know how long it might have sit somewhere with a missing turret ring cover?? My truck was runner, low miles (1200 miles, 200 odd hours). Pretty good shape overall, just lots of aging from sitting and sun
Make sure under the dash you dont have corroded or loose connections. I found the starter switch on dash had at least one wire a little loose, and a couple corroded.
Oh yeah, just out of caution, if I were you I'd check the other end of that wire going to alternator, make sure its tight, clean. I'd double check the alternator connectors too, make sure they are tight, clean (theres a couple specialty connectors on top of alternator, would be easy for one of them to be loose, they have locking ring on them that just turn to lock in place.... could have one pushed in place, but not locked, and it could be bouncing around, making intermittant contact.
An easy way to check big alternator wire might be to just run engine, and check voltage at each end of wire. Should only have very small voltage difference between ends (like .1 or .2 volts max). That big of wire should have low resistance, hence low change in voltage measurement at each end. Big voltage difference between ends would indicate its got high resistance somewhere.
Another wild(er) possibility could be loose belt causing alternator to have some slippage, have fluctuating speed, hence fluctuating voltage? Probably not, but these do have manual tensioner.... and I know mine has 300 amp alternator, at 28V thats 8.4 KW of output at full load, so its probably taking 10 to 15 hp to drive it, thats a lot of power through serpentine belt, esp with relatively small alternator pulley diameter...even with 12 ribs on belt, its a lot to drive, wouldn't be hard to have some slip with loose belt. Even the standard 150 amp alternator is nothing to sneeze at, since its 28v... that would be a 300 amp alternator at 12/14v... which is a good sized alternator, take a not tiny amount of power to spin it.
One last thing, theres a... "thing" back by the battery box, its like a big block of maybe brass (or maybe its just brass where the big wires connect). The big ground cable to the starter comes from here, and this "block" is fed by big wire coming off ground battery terminal. One big wire in, one big wire out, and two small wires that go... somewhere. I know all this because I had to unhook the cable going to starter to replace said cable. And I have no idea what exactly that ... block... does. Could just be wiring terminal block, convenient for manufacture when installing components....not doing anything but providing place to bolt components to, provide ground to them... but if I was chasing grounds on one of these trucks, wouldn't hurt to check it out... again tight clean connections if nothing else...
Well, i'm just rambling by this point. Just had a bunch of thoughts relating to this that I thought i'd share (esp since I'm currently working in this area.... tonight I might be making those big cables and putting them in). Steelsoldiers has been a great site for me, tons of great info here, learned a lot from this place (and had people from here help me, just had someone send me some very nice files today in fact), so when i can pay back the site by giving out some info / ideas.... i try to do that
PS. This might be something that you know (or can look up easily) Whats the part# for the starter? OEM vs replacement? Just asking in case I needed to replace mine (since it seemed to turn over a little slow). I looked on cat parts online, just couldn't find the right one (sometimes cat parts online is hard to navigate.... but usually I can find what I need.... for starter motor it was just drawing blank, though I suspect the truck had one part# installed, and it was later updated with new part, part#... which can make searching more difficult (only the original part # might be shown as direct fit, the replacement may not be shown as direct fit)