I like the premise but the way it plays at the moment is either slow and tedious, or rage quit inducingly frustrating.
@Vinehead gave a very good review and covered everything I wanted to say.
You may not have made the assets you used but you have tied them together in a pleasing way, you might think my opening statement was a little harsh, but you have made a good effort with this, and I did spend a bit more time than I thought trying and trying again.
I do like the checkpoints as they mean that "death" doesn't mean you have to start the whole puzzle again. I did notice though that any enemies killed up to that point revive. It might be better if they didn't as this might reduce the amount of times you get spotted with the current set up.