Unless your a high level gymnast you will not "muscle up" by only doing bodyweight movements.
For the average weekend warrior you need to be hitting the iron hard and heavy for a few days and then backing off to allow your body to recover, rest and grow.
How about you try try training like this for 6 months:
Mark Ripptoe, starting strength or Defranco's West side for skinny bastards.
And how about you eat like this for 6 months:
Note* you haven't outlined your diet and by your post I'm going to assume your A) skinny and B) eat like a bird. If not please let us know so we can suggest something more appropriate.
Anyway try Mark Ripptoes Anti Skinny Fat Manifesto or A Cold Slap In The Beginners Face.
And how about you rest like this for 6 months:
8 hours of sleep a night.
Naps when you can.
Get in your active recovery I.e. Walks on your rest days etc.
Anyway, try that for about a year and you will be on your way to getting "muscled up"