Phew! I just read all 11 pages of this thread! I wanted to skip to the end to see how the story ended, but felt it better to read the whole book desperately hoping for a happy ending for all concerned. Alas, I was saddened to see that you're still in the process of getting your baby running correctly and hope it all turns out for the best soon for you. By all means, please continue the thread to conclusion; we all learn so much from these threads on how to deal with our own cruisers.
I have a similar problem and saga and am in the early days of getting to the bottom of it. Same basic deal though - I took my '97 Anniversary model with only 170K miles to a small shop that allegedly specializes in Toyotas and which came recommended (albeit not by other LC owners...). I was a little concerned when seeing the shop as it was not clean and appeared disorganized. Nevertheless, the shop owner had a good shtick so I let them do the head gasket job. To minimize chances of aftermarket junk parts being installed I bought and provided all the necessary factory parts for the job and usual "while you're in there" jobs (like the injectors, fuel filter, PHH, oil cooler, etc) beforehand from various Toyota online resources (ie McGeorge Toyota, etc). The truck spent four full weeks in (and outside) that shop as I'd told them to take their time and use it as filler work and do it right and by the FSM (which I also provided to them). On popping in one day to see how things were progressing it was clear they'd not followed the FSM since they removed the intake manifold without removing the throttle body first, even though I'd told them I wanted every single vacuum hose replaced with new since they'd have it apart anyway and even provided the tubing/hoses... As well, the head was off and the timing chain nowhere in sight, but the main sprocket laying on a cart, the tech said he had trouble removing the cams and dropped the chain into the front cover saying it was easy to fish out. So I asked whether he'd installed the service bolt on the cam sprocket and said no there was some wrong and couldn't get it in... All of this meaning he'd not read or followed the FSM in the slightest.... Probably just zipped all the cam bearing caps haphazardly as well...
Me = Not Happy. Shop owner, not happy that I was appearing unannounced... In then end I got the truck back and it basically seemed to run fine, but I've had an uneasy feeling about it ever since. And as I take the thing into the depths of Death Valley and on hard to reach mountain trails, not feeling comfortable about the engine is a bad thing, and I so wished I'd done the head gasket project myself. Oh well...
Fast forward 5 months and 2000 miles to September, I notice low to no oil pressure on a road trip. So I had the oil changed mid-trip just to make sure. (and now, with my 20/20 hindsight I should have had the oil changer give me the oil filter to study later...) Anyway, no change in oil pressure with new oil and filter, but the truck was basically running fine so I continued the trip and made it home. So now (March) 5 months and 2000 more miles later (and well within the 12 months / 12K mileage warranty for the work performed) I'm noticing some rattling sounds and still low to no oil pressure. So I do some research and conclude that I at least need to change the filter to a Toyota 90915-YZZD3 filter to see if that helps; and since I was at it, go ahead and replace the very inexpensive oil cooler and oil pump pressure relief valves and springs (all of which seemed to be in perfect condition...).
Well first thing was to drain the removed oil filter and noticed pretty sparkles in the sunlight as the oil coming out of it... hmmm not so good...
So next step cut the old oil filter open and see what's in the pleats... ugh, even worse news...
Thankfully (maybe), little if any of this metal responds to or sticks to a very strong magnet; so it seems it's all aluminum? But from where?
I drained the rest of the engine oil and let it sit for hours looking to see if there's any more metal in the oil pan that came out, again slowly dragged a magnet through that and nothing sticks. Good, maybe? So I slowly poured it into containers an see no additional sparkles or metal indications. Certain nothing like what came out of the filter. Not wanting to remove the lower (steel) oil pan, I stuck my endoscope camera into the pan to look for metal on the bottom; now these cameras are hard to use on a good day, but coated in oil laying under the truck they're near to impossible to maneuver into the right position to see or make sense of what you're looking at; nevertheless, after numerous tries I saw nothing like metal chips anywhere, gave up and refilled with fresh oil. I have saved the old oil and am waiting for my free Blackstone Labs oil test kit to arrive so I can send them a sample for analysis (probably along with a piece of the metal covered oil filter pleat...).
Oil wise I bumped the oil from synthetic mix 10W-30 from the oil changer to a synthetic mix 10W-40. Switching to the Toyota filter, replacing the relief valves and springs, and increasing the oil viscosity does appear to have improved the low oil pressure; it's anyone's guess as to which item was the low pressure culprit, but the end result is good, I think... It's still quite low at idle, but is at least back up to low-mid scale on the dash gauge at driving revs of around 2000-3000 RPM, about where I remember it being prior to the head gasket job. (And yes, I've removed and tested the oil pressure sensor and confirmed it's not faulty...)
Even with good oil pressure I am getting a rattle, not so much of a 'knock', but I'm no expert on what a knock might sound like and haven't gotten far enough along to determine whether it's a op or bottom end noise. However, there is some rattling after start up and some warm up that occurs as I increase the revs to to and then through 2000 RPM, but quiet down as I continue to 3000 RPM. When driving, if left in 2nd gear to facilitate back pressure deceleration, when I release the accelerator pedal quickly the rattle becomes quite noticeable. Otherwise, the truck is relatively quiet and seems to drive fine, but all that metal is deeply concerning and I certainly have no faith in taking the truck in to the wilderness where an extraction due to a failed engine could cost thousands of dollars.
So like the OP, I am now weighing my options on just how to proceed with the shop who did the head gasket. And as the others have commented, I applaud your patience, even handed and non-adversarial approach to dealing with your head gasket shop owner.
If indeed this metal is bottom end related (rod or other bearings) what could the head gasket shop have possibly done wrong to trigger or cause such a failure?
If not caused by faulty workmanship by the shop I imagine that I'll just have to accept that it's just a coincidence that the engine is having a meltdown earlier in its lifespan than most, then get on with the fix, whether that be rebuilding it or replacing it altogether.
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