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If you have User Shares enabled then it is normal for every top level folder on a drive to automatically become a User Share with default settings and Unraid has always worked like this. 

The only mapping you have is to /mnt/user which is where User Shares are mounted.   Local drives mounted by UD appear under  /mnt/disks and remote shares under /mnt/remote.   If you want Krusader to be able to access either of these then you need to add volume mappings to support this.

Yes.
 
Click on the boot device on the Main tab and you can then set the SMB security setting for exporting it as a network share with the level of security you want to apply.

The syslog shows that you have docker set to use macvlan AND have bridging enabled on eth0.  As mentioned in the Release Notes this combination is know to cause system crashes.    You ether need to disable bridging on eth0 or switch docker to using ipvlan networking.
 

I think it should be 0 3 * * *
Note that space is a field separator so there should be 4 spaces between the 5 fields.

Both the links you posted go to obsolete documentation.  The online documentation is accessible via the ‘Manual’ link at the bottom of the GUI or the DOCS link at the top of each forum page. The Unraid OS->Manual section in particular covers most features of the current Unraid release.
 
The section on replacing disks is here.   You will need to upgrade parity first as no data drive can be larger than the smallest parity drive.

Have changed the SMB Export option for the shares you want visible on the network?   The default is No which means they are not visible on the network.

You could use a Trial licence to build out the new machine.
 
On completion you could then copy the 'config' folder for the new machine (except for the trial licence key file) to the flash drive with the Pro licence to transfer the settings of the new machine to it.

The Release Notes mention that if you want to use macvlan then you should disable bridging on eth0 to avoid crashes that can eventually bring down the server.   According to the diagnostics you still have it enabled.

The 61% relates to the amount of space used in the docker.img file.
 
You should post your system's diagnostics zip file in your next post in this thread to get more informed feedback.  It is always a good idea to post this if your question might involve us seeing how you have things set up or to look at recent logs.

That means that you almost certainly feel foul of the behaviour described in the Caution in this of the online documentation accessible via the Manual link at the bottom of the Unraid GUI. 
 
If you had used something like Dynamix File Manager plugin to do this it would have protected you from this problem as it always uses a copy/delete strategy for moving files.
 
You can use Dynamix File Manager to delete the empty folders.

It could be the Cache Dirs plugin which would keep issuing 'find' commands to try and keep directory entries in RAM.    It is a good idea to configure that plugin to only scan folders that need it as it does not work very well if there are too many files/folders in the ones it is scanning.

That shows that the Connect plugin is the culprit.    The most recent update to that plugin fixes the excessive logging issue, but you will still need to reboot the server to clear the log space used.

I think the problem is all the disks are now showing:
Formatted with type 2 protection I do not know if this can be removed and keep the data on the drives.

1.  Yes
2. You can give the licence files different names to help you tell them apart.   When transferring licences you put the licence file for the one you want to transfer into the ‘config’ folder on the new USB drive so it knows which one is being transferred.

You will need to contact support to resolve this.
 
Have you already used the 1 automated transfer allowed per year?  When that is exceeded you always need to go via support.

You will need to run without -n or nothing will be done.    If you get prompted for it then add -L.

A rebuild does not clear an 'unmountable' status as a rebuild gives you exactly what you can see before the rebuild.   The process for handling unmountable disks is covered here in the online documentation accessible via the Manual link at the bottom of the Unraid GUI.  In addition every forum page has a DOCS link at the top and a Documentation link at the bottom.   The Unraid OS->Manual section covers most aspects of the current Unraid release.

If you go the New Config route you can remove them all at once as after going this route you will be rebuilding parity to get your array back into a protected state.  You are unprotected until that finishes.  
 
An alternative process in the first place would have been to use New Config to both remove the old drives and add the new drives at the same time before copying/moving any files and then rebuild parity based on the new set.  You could then have mounted the old drives one at a time via the Unassigned Devices plugin to copy their contents back to the array.  This would have been the fastest approach although you would then not be protected against one of the old drives failing before you copied their data back to the array.
 
If you want to remain protected all the time then you need to remove them one at a time.
 

You need to reinstall the binaries for your docker containers (with previous settings intact) via Apps->Previous Apps->Docker.

It is a requirement of Unraid that each drive has a unique ID (typically serial number).   It looks as if the USB3 chassis you are using does not pass through the serial numbers and has given both drives the same ID.   The only fix to this is a different USB3 chassis that DOES have unique ID's for each drive.

Yes.   You only want the driver if you intend to use the GPU in docker containers.   If passing it through to a VM you do not want the driver.

You seem to have a network problem limiting your speeds.  It is as if you are only connecting at about 100 Mbps.
 
Have you tried alternative LAN cables and/or ports on the router?   If not all ports on a LAN connection are connecting the speed will silently degrade to 100Mbps as that connection needs less active connections in the cable than is required for 1000 Mbps.

Put the extra disk in a pool;  Creat a Downloads share which has the pool set as primary storage and no secondary storage;   Set the media share to have the pool as primary storage; the array as secondary storage and mover direction to be pool->array.

You seem to be getting continual resets on disk3 which probably explains the slow speed.   You might want to check the power and/or sata cabling to the drive is well seated.  I assume the PSU is up to handling the extra drive?
 
BTW:  You probably need to disable spindown to get the Extended SMART test to complete.   If the drive cannot pass that it will need replacing.