Hey Nick ,When instaling the cut down screen into my ute we bashed it so hard with the mallet that I expected it to break and was very surprised it didnt.
The utes got laminated glass and you are using toughened glass which has differnt characteristics and is genuinely a lot stronger.
I doubt you will damage the glass unless it has a pressure point somewhere and you will realise straight away if this is the problem because it will shatter immediately.
Using your feet is the way to go and try soapy water in the seal before you place the rope in.
I also pulled the rear side windows out of my wagon a couple of weeks back and they came out front first so I would install them in the reverse order - front last in.
Good luck Ill keep my fingers crossed mate