Maintenance chaos
The VC-9 flush combo is done with the t/stat in to the bottles' instructions....the vehicle is driven until it comes to temp.....the draining process begins, the t/stat is removed, the block drains are removed (and replaced with fumotos that fit those thread pitches for future drains) and the system is flushed thoroughly with distilled water for a while until it runs clear. The oil cooler is changed out and the system is topped up with ELC concentrate (3.5 gallons I believe) since the block is full of distilled water already and then the coolant is tested to confirm concentration.
I probably missed some steps but in a nutshell I think that is it. The block cleaning/flush is sure to destroy the oil cooler from what I read.
Good Luck
Just an fyi your more likely to overheat an engine with out a tstat then with one
You described you ECT/EOT split as "marginally out" so I'm assuming you see 15+ degrees difference unloaded, fully warmed up, 65mph, on flat ground, or it's close and you've been watching the temps rise over time and you can see it will be going over 15° soon. It's important to be as accurate (and honest with yourself) as possible when taking the measurement, we have several posters here who have had 10°+ for many thousands of miles with no increase in the split. Being close doesn't count unless you're watching it rise over weeks or months and can see where it's heading.
If you're going to change the oil cooler, flush the system with chemicals before starting the work. If it's bad enough to clog the existing cooler it needs cleaning. The exception to this is when there is oil in the degas bottle. If it's leaking (oil) badly, it will be impossible to get it clean while the running the engine is pumping more oil into the system so you're just chasing your tail. If it's just a few drops floating on the surface of the coolant in the degas bottle or even a light film, now it's a judgement call.
SrMasterTech has a two part video on the flush procedure on YouTube where he shows revving the engine with the block drains removed. The flush water is blasted out of the drains with a lot of force and I believe that's a big help in removing solids from the block "skirt" area of the cooling system where much of the trash settles. In our Tech folder here in the 6.0 forum there is a very complete set of instructions (thanks Nylyon) that is well worth the read. Pay particular attention to the discussion of alkaline vs acidic cleaners and when to use them.
So to sum up, be sure what the temp spread really is.
Check the video's and Tech folder. You may have more questions after that.

If it's less than 15° but you're not comfortable with it, drop the coolant, flush with water (all distilled or a garden hose and distilled immediately after), skip the chemicals, go back with the same type of coolant that was in it and keep your fingers crossed.
If the number is 15° or more flush with chemicals, change cooler, and go back with your favorite coolant (as long as it ain't green or orange). I've yet to see anyone claim to clear a clogged cooler for a significant time and we've had several who were very determined. It's possible to drop the temps for awhile by flushing if that helps your situation but EOT will come back up pretty quick.
As far as the thermostat in or out, you're right that it will never reach operating temp with it out but I don't think it matters much. The reaction may be quicker with it warmer but the chemicals will react with the corrosion even if the water is cold. It's just a matter of how long it takes to do a thorough job, if it warms up to 120-130° it's working well and water flow will be better with the stat out of the way. Cool down will be quicker so draining won't be as dangerous, and you won't have as high thermal shock to the engine parts when you put more fresh water to it.
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