Manifold Update:
I partially installed the manifold without gaskets. The center section installed cleanly. Initially the rear section had a gap, however with very light torque that section also closed to no measurable gap.
Initially the front section had a gap but that was due an alignment issue and the edge was cought on a ridge of carbon.
Cylinders 3, 4, 5, and 6 are B+ or better on both the manifold and head. #2 is a C- on the head, there may be remaining original gasket remaining on the head. #1 is a different story. The manifold surface is not smooth, there is an edge on the outer edge, and the head shows some corrosion.
You've got to end up with a sealing surface. I don't know which type of gaskets you have. If it's the MLS (layered steel) gaskets, you've got to above all else preserve the "ring" where the ridge makes pressure. If you've got "conventional" gaskets, you need a sealing surface all the way around. And you've got to get them close enough to one plane that the manifold can reach without undue stresses.
There is recent opinion that it is not best practice to use an air rotary tool to clean these surfaces. I plan to make a light pass on #2 and a pass on #1. I look forward to your inputs.
You're gonna get me going.....
That's not a recent opinion, that's been a fact since they invented the things. Those things have no business near an open engine. That is the WHOLE story. The beginning, the middle, and the end. The reason it's still a discussion is because it's easy to make shiny. The only opinions "endorsing" this are from people who take lazy over facts and evidence.
That said..... You're working on a coach, not a line haul truck. A million miles isn't going to happen to that engine. Access can sometimes be more expensive than a full on recovery from bad practices gone wrong. Life is hard, and sometimes the lines are blurry.
On the engine side, you can not let that debris (somewhat the metal, but mostly the abrasive residue), you can not let that get into the exhaust ports. Even the ones that look closed.. That will get pulled in (yes, pulled in. Before the engine starts, due to the normal leakage of the rings, there's a small but surprisingly tangible vaccum pocket there at teh bottom of the "would have been" power stroke) to the cylinder as you start the engine.) All that stuff that won't blow out (dust mostly, chunks will blow out) It gets sprayed out of the air by the diesel fuel and will be on the cylinder walls from now to the end of days..... You've got to stuff the ports full of "something" that's going to keep it from getting down in there. Once it's down by the valve/seat area, you're not getting it out.
The manifold is a bit easier since the turbo is off of it at this point, so long as it's not all slobbery in there, you can clean it pretty easily. And if you don't, it's not good, but it'll pass. For a low miles engine..... I wouldn't sweat the grit so much on that one.
And then the "flat" thing... If you're using a rotary tool to make a flat thing, you will fail. If you're using it to grind off "stuck gasket" or "stuck carbon" or a rust ridge, or whatever... At the same time it's taking the metal in the local area around that So by the time you flatten the "bump", you've made a crater on a larger scale.
All in all, the cookie discs and the whisker biscuits (and whatever cool name's you've heard for them...) are best reserved for SMALL removal, or even just softening of high spots so that the gasket can do it's job with some degree of durability.
Were that me, well, I know it's not an ideal world, and I "might" actually be convinced to turn to something aggressive like that (and potentially dangerous to the engine if it's not respected). I wouldn't use it for bulk cleanup at all, but for "touch up" level work. That's where you see the predictable, big (expensive) comebacks is when somebody thinks they can deck the whole right side of a cylinder head with a tool like that... Folks that "get away with it", myself included on occasion, know and respect the risks as just that. The risk that something gets by you or gets away from you. That approach tends to have a lot less odds of having tangible repercussions.
The typ of wheels you use, if you're gonna, (which I recommend against, but again, real world compromises are a real thing some times...), let me clear up another "opinion" thing...
There are NO safe wheels. Depending on who you talk to, you will likely find that WHATEVER their favorite type of disc is, that is the "safe" type. It's not opinion, they ALL do this. They all throw microscopic and macroscopic "swarf", and they all shed abrasive..... I'll tell you this though, first of all, brand matters. The cheaper they are, the worse it gets. Second of all, the "surface conditioning discs" (scotch brite discs, "cookie discs", etc) shed a LOT of dust, a LOT of abrasive impregnated fiber filler, and make a HUGE mess. 3M "Bristle Discs" (whisker buscuits) still make a mess, but they throw "less" abrasives. (Yes, they are impregnated with abrasives). Those will still not be "safe", but they are by far the most managable option if you have to make stuff happen... The "green" flavor is the one you want. It still leaves a finish that a gasket can seal to with no sealer (that would burn right out where you're gonna put it...), but it's aggressive enough that you can get a high spot down easier. The finer ones... Somehow, some way, the finer grits end up making the big crater around the little bump thing I mentioned even worse. I guess yo've got to have something aggressive enough to just get in and get out... And like I said, brand matters here. Other brands may be equal or better, but I couldn't tell you which one. Typically, when I find a brand of "somebody" making one of these bristle discs that look like the 3M thing, whatever you run it on just ends up with a white, red, yellow, or green shadow over everything in the vicintity... So hence my preference for a "go to" when I've got to do sketchy chit...
One other thing, as you're looking for buildp/rust/scale/old gaskets, and trying to distinguish that from actual metal high spots- Anything that's "on" the metal is (probably) brittle. I use a teeny, tiny little ball pein hammer a lot. Or I'll tap on half of a needle scaler needle against a surface. Rusted scale willl come off in chunks that way. Just be respectful, you're not looking for a golf ball finish on the rest of the metal. Another tool that I use a lot for manifold/exhaust joints is a cheap, crappy, stinks like baby vomit wood chisel set. I made gasket scrapers out of them. (Basically just a little angle on the "flat" side so they skate flat on the part while your hand is around the handle). Those are "strike through" with a metal cap for hitting. Given that they're cheap, both quick and EASY to sharpen (something flat with sand paper on it...) I take a LOT of manifold/turbo/exhaust flange crap off with those chisels. Don't "hammer", just "tink, tink, tink, they do quite well. It wrecks 'em quick of course, but a quick swish on the paper brings 'em right back. The chunks o' crap stay larger (safer for an engine than fine stuff), and it minimizes, if not eliminates the need to resort to other options.
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