"#>" Denotes a console command
1) Deny access to MySQL over the WAN using iptables
#> iptables -A input -p tcp --dport 3306 -j DROP -i ethX, where ethX is your external interface.
#> echo "iptables -A input -p tcp --dport 3306 -j DROP -i ethX" >> /etc/rc.d/rc.local
2) Create an stunnel certificate
You must have "make" installed, so you may need to install make and other related tools.
#> cd /usr/share/ssl/certs
#> make stunnel.pem
Your common name should be the FQDN (fully qualified domain name) for the host that you will use.
3) Create a hosts.allow template fragment
#> mkdir -p /etc/e-smith/templates-custom/etc/hosts.allow
#> cd /etc/e-smith/templates-custom/etc/hosts.allow
#> pico -w SecureSQL
Add the following line:
ssql : ALL
Hit Ctrl-X to save
#>/sbin/e-smith/expand-template /etc/hosts.allow
4) Start stunnel daemon
#>/usr/sbin/stunnel -d 57600 -r localhost:3306 -N ssql
#>echo "/usr/sbin/stunnel -d 57600 -r localhost:3306 -N ssql" >> /etc/rc.d/rc.local
Now, 3306 should be denied from the WAN interface and 57600 TCP is a stunnel daemon that is wrapping to 3306 as localhost (no transparent proxy flag set, intentionally)
For your linux client, you simply need to type:
#>stunnel -c -d 3306 -r SERVER:57600
Now, localhost:3306 redirects to 57600 over stunnel, which then redirects to your server on 3306.

Now from the client, you can access your mysql database while enjoying the benefits of SSL encryption with the mysql client with the following command:
#>mysql -h CLIENT -u YOURDBUSER -p
The same command would hold true for your Windows client, you just need to find a Win32 port of stunnel. I'd be more than happy to email it to you if you want.
Note my lack of experience with 5.6 may be an issue, you may need to open 57600 using iptables.
Hope this helped,
Nathan