Welcome to wargaming Age of Sail in the Grand Manner, it sounds like you are hooked!
If you don’t want to use the plastic ratlines, there are the etched brass offerings from Meridian and I have seen a device for stretching lines of thread over to create the pattern, on one of the 3D printed ship sites.
The work Tom Jensen did pulling together the ship stats for WbS is truly impressive and as you say worth the cost of the rules for that alone, that said we have had a lot of fun messing about with them and Tom has been very generous in observing and commenting on a bunch of inveterate rule adaptors as we have played about with his core system, but I think that argues in some way to their strength in that you can tailor the rules to what you want without losing the essence of what attracted you in the first place.
Like you, we have had conversations about the cluster of markers that can blossom around models as the game proceeds, but there is the option to use record sheets instead and one of the chaps in our group thought about using different coloured mini-dice for crew, hull and rigging hits to carry on the bases as perhaps less obstrusive.
I haven’t settled on any particular way yet and am focused on the playing and rule adaptions we are creating before getting into thar particular process, but I’d be interested to see what you come up with.
It sounds like you have plenty to get on with and I look forward. To seeing some pictures and a write up on the blog.