It's definitely more organised now. Just make sure it doesn't get a mess: if you want to change something later on, than you don't want to search for a snippet of code.
Personally, I would not put such a huge block of HTML code in a 'global' file, but that's just me. I have got no idea how the rest of your code looks like so maybe this works very well.
I wish you good luck with the project and I will come back here to follow your progress, every now and then.
I've got one final question. Do you have a clue on when you are going to finish this project? I know it's very hard to give a date, because 90% of the developers can't make a certain release date (or at least not without rushing) but perhaps you can supply us with a wider timeframe. This year? Q1 2012? Q2 2012? I'm looking forward to go through your code once it is released.
Don't give up!