Matej, I've had a look at the screenies, they look really nice. Great work already! Now the question: could you upload the templates (photoshop?) to the forum, so I can try your paint in FS and see if it needs some adjustments. I've just enabled your right to attach files to forum posts, so you should be able to upload them here.
What I can say from the screenshots: the belly and the curved line are perfect. The nose should be entirely white, imo, and the engines maybe more like the 738 - see here: http://www.air-child.com/preview/repaints/738pmdg.htm
I also thought there was a problem with alpha channels but I just reread your post and seen that you made 2 versions for the body. Personally, I prefer it white. Other opinions are welcome, though. I think only AA has that shiny metal look with their Maddogs (or what's left of them).
btw: is this the Flight1 MD-80? FSX or FS9?
Concerning a cargo paint, Tobias is right. There's no MD-80 freighters. That means less work
Many thanks already. Looking forward to see your templates.
Peter