I doubt filling the reservoir had any bearing on your PTT system. The reservoir is open to the air and self-bleeding. You should be using auto trans fluid or SAE 5W-30 motor oil, whatever the unit already has.
The special tool is kinda like a funnel which has a small taper. It compresses the Teflon seal on the piston, as you push it into the cylinder liner. I never had the tool and after ruining the Teflon seal trying to install it, I had a Merc Dealer install a new Teflon seal for me, using his special tool.
It is likely only one piston seal is leaking, however, there is no easy way to tell as they are connected together. You could remove the hydraulic lines for one cylinder at the control valve and plug the control valve and test the other cylinder for leak down. The plugs are standard NPT I believe.
The hydraulic lines to cylinder threads are pretty fragile. They strip easy, so be real careful when removing or reinstalling. You have the cylinder bleeding procedure? They are not self bleeding.
Scott sounds like he has a line on the rebuild kits.