yah i know i'm anal about my diy projects as well. painting these will actually fall nicely in line with some other projects i have to do. i've got a lot of work to do on my door panels so those are coming off anyways, and i'm installing sidemarkers in the fenders so i'll be working that area too. only thing out of the way are the rear quarter. and i've already popped out those interior peices twice before. didn't totally pop them out but enough to get my hands back there.
so you didn't break any clips or anything. also, could you elaborate on what you meant by you have to slide the molding to one side. not sure what your talking about.
also, you might want more than one layer of clear coat. these can have a lot of hits on them(thats why they are there) and one layer of clear prolly will not hold up to some of the hits which means chipped paint. also with more clear you can get it to match the gloss of the rest of the car.. just some high grit sanding and some rubbing compound

but i'm sure you already know all this.
pics would be cool too.