If you keep the clouds perhaps think about some dithering to blend them in a bit... If you're trying to improve on the graphics further, Its presently pretty much the same as the arcade and looks great, but there's not much detail on the underside of the roof either and enough colours in the palette to add some flood lights, some more panels/structure there, keeping the contrast on any additional detail really low of course.
I'd perhaps be willing to have a go myself, (just to improve the clouds perhaps) using a real a1200 and my amiga tablet + deluxe paint. I work professionally as an artist for 10 years, and have worked in the games industry on everything from Indy's to AAA productions.
I understand that the team probably has all the people they need, my contribution may not be wanted, and I couldn't promise a lot of time to devote to it, nor would I want to butt in on someone's territory either, someone who's probably invested a lot of personal time so far... so my apologies to whoever is concerned (Turrican 3?).
Might be fun though.