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This Question is a bit older, but for other users with the same question:

You can just enable TLS in pureFTP like you would if ajenti was not installed.

Ajenti does not mess with your pureFTP configs..

For basic managing of additional ftp users, you could use my bash script, which can be included in ajenti:

Yes, full IPv6 Support for web-, mail- and ftpserver.

In general it should nowhere be a problem, because for example in the website administration, you enter the listen address manually, so you can enter ipv4 and ipv6 types.

I am using a standalone letsencrypt client.

I have my certs generated to /var/ssl/certs and provide that path to the ajenti nginx config.

maybe this is an option for you, too..

This is the client i am currently using (it is simpler that the official one..):

I don't know a solution for your problem right now.. You should double-check that you have edited the correct place for the password, maybe the same password is used at different places in the config file?

I will try the solution if i am back home today evening and write you an answer later.
Please have a look at this wiki article:
You have to reload the ajenti-v config by using the command ajenti-ipc v apply
If you have some experience in server administration and programming, you could try to update the config file from ajenti-v.
It is located in the /etc/ajenti/ directory and is in JSON-format. You could try to parse/change it using for example php or python.
I missed that you want to redirect all subdomains to your main domain.
For doing that, you have to create a new site and add the alias domain i have mentioned above. You will use this site only for redirecting. In this site, you add the following line in the "Custom Settings" box in the "Advanced" section:
rewrite (.*)$1 permanent;
You are right, the approach i suggested to you will not work if you have multiple domains set up on your server.
But the way you described above has worked for me right now.

You add "*" to the domains of the site, you want to catch all subdomains for.
Subdomains you have added to another site will NOT be catched by that wildcard entry (checked that).
Make sure that you click the button "apply changes" at the bottom of that page.