AusBonsai

A very dear friend gave me this little JM 3 years ago. Its 7 yrs old. Its oddly shaped for a JM but I like it, and have a very soft spot for it. I want grow it small and petite. Its 175mm high at the small red line I've drawn (pic 3).
I'm on the lookout for the perfect rock to place under the trunk, so it looks like its grown around it. There is a reasonable rootspread down there. Will be working on it this season....
I would really like to know what you think of it, and also some advice on how I should proceed with it. I want to grow it according to its natural style so any opinions would be appreciated...
Something that really bothers me is the long internodes (especially the top one in the trunkline). I had it in the ground for last season. I'm thinking of cutting them short and start growing it again, but then again not sure if I should do that.....?

First rule: If you have a problem cut it off. No more problem.

You are correct about the long internodes. You will need ramification in a small tree. You will not get buds between nodes. Therefore cut off those long bits and regrow them. You will probably find that the new shoots will also have long internodes but cut them off again, this time after the spring flush. Then it is more likely the tree will give you some shorter growth.
You are also likely to get lots of shoots growing from the node you prune back to and you MUST thin out the new shoots down to 2 or 3 initially then to just 2 by winter. Leaving lots of shoots from 1 place will thicken the ends of the branches and looks terrible.
I think natural shape of Japanese maples is multi trunked but small bonsai JM look good as informal upright as well.