Thanks for pointing me to the Wilson Cycle theory, it's been very helpful in understanding things more.
After reworking most of the plates, and some more, and then some, it seems there's just no single combination that would reasonably explain the formations on my map.
If I understood the WC correctly, to form one of the mountains on the center continent it would require:
- any plate large enough to stay 'intact'
- a small plate the size and shape of the mountain to collide with the above plate
- This small plate would then need to subdue the other plates that collide into it and keep rising
Basically, it's a chain collision where the first few pieces are smaller than the (resulting) mountain and where the last plate forms the land as it is now.. This would be a maze of tiny plates that somehow become a coherent one (not unlike a tiny super-continent)
This either makes no sense or is so unlikely that it would not happen a second time 'nearby' (some 900km away) and a third time (also some 800-1000km) all on the same continent...
Quote Originally Posted by Shikotei
If these mountains make no sense after this, it might be time to remake the map(..)
Sadly, this may have been the inevitable result of using a generated method.
Large - Tectonics v02a.jpgLarge - Tectonics v02.jpg
The above maps represent my latest attempt at getting most of the existing formations to make sense. Not everything can fit, so I've accepted that I will have to make the map again, but this time based on tectonics. Effectively I would have to recreate the height map (which I will do using the existing one).

Just to stress this: ignore the rendered features, I'm starting from scratch. The left image is only posted to give an impression.
The coastline and a desire to keep some of the features intact (either on the same location, or re-located) are all I will use.

As for the new what's-what:
- the grey smudge would represent the 'logical' formation of mountains.
- the purple numbers are there to easier identify the plates

Now for the descriptive reasoning behind the choices and what's happening where:
Plate 1 is colliding with 4, having filled the now-gone water basin, it created a mountain range on the south side of plate 1. Plate 4 is being subdued.
Plate 2 has done the same thing plate 4 did to 1, creating a mountain range on the north of 5a. 2 is subdued here.
Plate 3 is drifting away, creating a rift near 5a, 6, and 7. The hot-spot created a chain of volcanoes (of which only one is still active).
Plate 4 is rotating clockwise, colliding with 5a and drifting from 5b. 5a is subdued. The hot-spot on the southeast created islands.
Plate 5 is breaking apart into 5a and 5b at the point between 5a, 5b, and 6. Plate 2 is pushing it southward while plate 9 is pushing it northward. The large fault line [and its splinters] are the result of this breaking. The center of 5a has a large caldera (super-volcano maybe?)
Plate 6's collision with 5b created a range of mountains in (again) a way like 1 and 4, and 2 and 5a. 6 is being subdued.
Plate 7's collision with 10 did the same. 7 is subdued.
Plate 8 is a new plate (broken from 5b), currently expanding between the rifts that [4 and 5b]'s drifting created. Active volcanoes expand the land even more.
Plate 9's northward drift (and oceanic character) causes it to be subdued by plates 5b and 10.
Plate 10 is drifting over another hot-spot, slowly creating more islands.

It could be that the mountain ranges created by the collisions of [1 and 4], [2 and 5a], [5b and 6] and [7 and 10] (is merging)/(has merged) the plates together, reducing the number of plates.
I may also should have drawn the plate boundaries between [1 and 4] and [7 and 10] closer to the sea-side of the subdued plate.. I'm unsure of this.