Sitewide file upload and assignment editing permissions - after upgrading to Moodle 3.1.x

Its all good.  I have been supporting moodle for many years and have been upgrading them too.  Last week, I updated one of the moodle's and my customer reminded me about some priviledge he lost.  It was as if he knew just where to look, like this exact thing had happened previously. ;)  Yes, the had.  I actually found a reference to the behavior in another post.  Anyway, the takeaway is this.

Upgrading the moodle and excepting the new site wide defaults upon completion of upgrade, causing a couple settings to be overridden.  I think.

My teacher responded the next day and told me he had lost a couple abilities.  This is his response.

Good Morning! I do have to agree that how the actual page looks is cleaner, less busy, and probably easier for students to navigate once they get used to it.  But I do have a couple of questions/issues that you might be able to help me with. First, I see that there is discussion of commenting inline on assignments, but I cannot find where to turn this option on when I create an assignment. The documentation does mention something needing to be set by the Moodle Administrator. I used this feature a lot before it was lost in the last update, and was excited about getting it back--am I missing something or is there something you need to do to allow me access to it? In a related note, the feedback text editing options seem to have lost the choice of changing the font color, which I have used a lot, especially because I can't comment inline naturally.
 Second, although I can still set upload size limits in my course administration, I have lost the ability to choose the higher limits in my assignment creation. There used the be a choice called "advanced uploading of files" that would allow me to choose a higher setting than 1 MB. As I have students submitting multimedia work, 1 MB isn't enough for some of my classes. Again, am I missing something or is this an ability that was lost?

After confirming what he reported by logging in as him and looking / recreating the issue, I was able to solve the problem by changing two of the site level administration options.

Site admin | plugins | assignments | Feedback
Site admin | plugins | assignments |  Files

The assignment activity has so much capacity, that each of his questions had their own path - area in the assignment administration.  This is where Moodle gets a little too complicated because of all of its options.  But, I activated the in-line feedback option and the file upload override.

Moodle - feature rich and convoluted.