[The Sheene Machine]

From the wip pictures it does'nt look like your doing anything wrong, clean paint, correct colours, nice looking build.
For seam filling I used to use putty's etc, but found similar problems that you have. Now I use super glue, dried off quickly with zip kicker. I glue to two parts together (super glue) and then sand the seam a little. This helps key the part. I then run a line of glue along each seam using a cocktail stick and then cure with the Zip Kicker, It instantly ready for sanding. I then gently use a 600 grit paper to level off the glue and finish with 1500 grit.
I like the fact that you dont get air pockets with glue and for me this method adds strength to the joint too.
On awkward areas I just use rolled up sanding paper (the wet n dry type) on a cocktail stick.
I've used this method for some years now for basic seam work and it's never failed me.