The values of settings should be maintained through version upgrades. The transition from 3.x to 4.0 will result in some non-reversible changes and some resetting to default values due to the nature of the settings changes in 4.0. However, from 4.0 to 4.0.1 there should not have been any settings change from what you have set them to.
I just did a test on my testbed with a 4.0.1 to SVN trunk “upgrade” with the values of several of the settings you mentioned changed (all of the ones that sit under the miscellaneous tab). The values remained what I set them to in 4.0.1 when I did the settings migration.