Firstly what was I thinking with my two pieces or perspex hinge thing, yes I needed to bend the silicone to pull on the rods but up is as good as down. I could have used a single piece. That is what comes with doing things on the fly and being seduced by "clever" ideas.
As expected the rods did come out and to be honest as expected it did take a bit of a toll on the silicone, I think a primer should probably be used to keep it well stuck to the perspex and apparently they are available. There were also a few bits of silicone pulled into the channels by the rods so if something like this method were to be used the other ends should be encapsulated in silicone.