I finally was able to figure out all those puzzles last night. On the Giant Bomb review they talk about how you feel like a genius when you solve a puzzle you once thought impossible. I actually felt like an idiot for not seeing the solutions the first time I played. I had the most trouble with world 4 and the least with world 6. It could have something to do with the fact that last night was the first time I played the game without drinking something alocoholic. Seriously, Braid goes well with a good merlot.
So the ending confused me. I've got a good idea now that I looked it up online, but I thought I had solved all the puzzles in the game. I was ready to let my mind rest a little and the game overloads me with information. My mind struggled to process it, failed, and then I went to bed still trying to sort it all out. I'll probably give the game some more time as I reread some of the story and form my own theories as to what happened and why.