I attached the transparency to the acrylics using spray glue. It was a hard to fit it at the first try and it ended up slightly crooked, but not too bad. The glue did make the unpainted "windows" for the displays slightly cloudy but that have to do for the time being. If I make another panel like this I need to come up with an easier solution.
For the thruster control I needed a potentiometer with a lever mounted in 90-degree angle to the pot axis. I simply drilled a hole straight through it and attached a spare Dremel spindle to it. Problem solved.
The pot what then epoxied to a piece of scrap PCB that is securely held to the acrylic by two of the push buttons.
For the thruster handle I used a piece of a "touchscreen pen" that I glued to the end of the Dremel rod. All in all I think it looks fully acceptable for something done without any proper equipment.