Alright Michealgr!
Here's a couple of images that I hope help with guidance on how to build the stays and hab modules.
The model I built shows areas highlighted with red circles as having the stays penetrate through the part. (Guide 1)
If I remember correctly, these are
The missile / torpedo pods
The main bridge
The sensor module which I believe I labelled as Pod 1.
I've included an image of the blender model minus the hab modules to show how the model should look prior to attaching the hab modules (Guide 2). The stays have a red highlight on each of them. Basically this indicates that the stays are designed to penetrate the full length of the parts and are then, attached or anchored to the interior of that part on the opposite side from where they are inserted (I hope that makes sense).
Some of the parts I am sure have included interior support sections (pod1 and the missile / torpedo pods) the purpose being to make sure the angle was of the struts was correct as well as give them a little extra support.
The Hab Modules themselves are attached directly to the stays, the areas highlighted with blue rectangles / squares on my model image (guide1). The stays DO NOT penetrate the hab modules. The hab modules are just attached / fixed / glued to the ends of the stays.
The stays were designed to be the correct length, however factors such as paper weight, thickness, build skill and my general lack of attention during the experimenting phase of this (seriously I wasn't even sure if the hab modules could be held by these stays without some sort of additional supporting parts) means that the stays may need to be trimmed at the edges to allow the hab modules to attach straight and true.
(don't look to close at my model but you can see one of the stays isn't quite long enough for the job and is clearly NOT attached the hab module
)
The image (guide 3) is the side profile showing the support stays for the starboard and port sides of the hab module / main hull. If I remember correctly I left two versions of this in the plans. The one I used was a single piece (highlighted in red) mounted to 1mm card then cut out and coloured using matching pencil, then trimmed as needed at the edges to fit.
In the plans they are unlabelled, but they look like the mage shown in (Guide 4)
I also left the individual stays in the plans for anyone ambitious enough to try and build this structure out of the individual parts