Activity

I think your approach looks just fine, you’re just dealing with a kit that has some irregular seams.
It was kind of a common problem with these mid-to-late 1990s 1:144 kits. Seams would flare out a bit or the surface would be warped slightly from the molding process, resulting in an irregular surface across the seams.
Actually, alignment on the 1990s kits can be a problem as well – and if your parts don’t align properly, sanding the seam smooth is really just gonna make a mess of it. It’d be like sanding down the curb to level the sidewalk with the street – the two surfaces aren’t on the same plane… So when you’re assembling you should be aware of alignment, and if necessary, cut off the snap-fit pegs and align things manually. I’ve not built any Gundam X kits but on the 1995 MGs, or the 1:144 Wing kits, I think this is essential.
To deal with these irregularities you can sand it until the surface is level with the sunken bits, or add putty to fill in the recessed areas.
Now, about your sandpaper – this may be a dumb question, but you mentioned 1200 grit sandpaper – that’s not all you’re using, is it? It’s very fine-grit, good for finishing, but bad for making any significant changes to the model’s surface. I usually start with 220 or 320, which would be very effective for leveling out the surface of the seam, and then progress through increasingly higher grits to smooth out the sanding scratches.
Of course there’s dangers in trying to level out somehting like this by sanding – you could wind up curving the surface or grinding down its edges – to keep a flat surface flat in this process requires some care. I think maintaining that control is easier when you’re doing coarse work with coarse sandpaper, because you can get the job done quickly, before fatigue sets in and you start getting careless.
Anyway, nice attention to detail. Good seam work is essential IMO – just a little hint of a leftover seam can totally ruin the effect.