Instead of saying that your machine is not designed to run at quarter throttle I should have said that your machine is designed to run 100% without overheating. If it is overheating so badly at far less than 100% usage it is likely that there is a problem with the cooling system. The setup you describe sounds good but make sure it is not clogged up with dust for example.

As to the file size, this will not change with the preferred run time. Rosetta sends a work unit, you machine will then process the work unit for, approximately, the time you have set and then send all of the results you have managed to generate back to base. The estimated time remaining will initially stay at 7-8 hours but will correct itself over the next few days as the system settles down.

Boinc not getting your credits could be one of two things, either you have not given that project permission to export your credits to the account manager or, like climate prediction, that project might not generate credits on a daily basis - it could, for example, be weekly.

I've tried to set the resources appropriately but it seems they do not work right. WCG seems no place to set this either, I must be missing it. I've never had so many cores to work with and with a high performance machine, so now I can do like 12-16 projects on an 8 core chip, but it gets way too hot, over 90C, even with just 8 running it gets to 70-90, I have to cut back. But that is a minor issue.
Ahhh, so on Rosetta, I can cut back the file size they send me? I didn't know that, I was wondering what the heck that was for, now I know and now I will change it to 2-3 hours per file. Makes more sense.

Log into the WCG website and select :-
>settings>device manager>device profile
go right down to the bottom of the page and change the project weight to 150 then save (assuming that you’re doing WCG and Rosetta only and that Rosetta is still set to 100 then this will give you your 60/40 split).
The main thing then is to wait, ignore one project or the other taking over the machine and it will settle down to your selected split over the next 4 or 5 days.
As to the overheating, review your cooling arrangement, make sure all the fans are working and are not fighting each other. Make sure all of the filters are clean and free flowing. Make sure the heat sink fins are clear of dust.
Big machines like yours are not designed to be run at quarter throttle so I’m guessing that it’s not working properly.

Ahhh, so on Rosetta, I can cut back the file size they send me? I didn't know that, I was wondering what the heck that was for, now I know and now I will change it to 2-3 hours per file. Makes more sense.

Or better still since running more than one project, set a small cache size & then let things settle down over a week or 4. Since you haven't run it for a while, it will take some time for the Estimated completion times to settle down, and for your Resource share settings to be honoured.

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