wow, that is a LONG time. I don't think you can run it via cmd, but I may be wrong.
Sounds like you have some really old pcs, you should consider upgrading them.
That will let you choose what to run and save it in the preset 0. Chances are when it takes 40 mins to open it wants to 'compress old files' so uncheck that.
Now actually run the clean preset with cleanmgr /sagerun:0
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