Tell me if I am wrong in this summary:
You had a linked GT. You change the Windows Live ID (WLID) of the gamertag (GT). This unlinked the GT from your Bnet account. You want to use your new e-mail but still have your GT linked.
If this is not correct, disregard the rest of this post and tell me I was mistaken so perhaps I can help you in another way. If that is correct, continue reading for your solution.
You can only change your Windows Live ID once every 30 days. Once those 30 days are up, change your Gamertag's WLID BACK to the e-mail it was before. That will relink your Gamertag to this Bnet account, OK? OK.
After you have done so, you need to go to the Windows Live ID Passport website. Click here for the link to the website. In the top right corner click 'sign in.' Sign in using your ORIGINAL (remember you changed your WLID back to what it was originally remember?) WLID and the same password. Basically treat it like you're logging into Bungie.net.
Then you will be taken to an 'account overview' page. At the very top of the page, the very first option, is your WLID (by now, you know this is your e-mail I'm sure). Click 'change' next to it. Change your WLID to whatever you wanted it to be for your gamertag.
The 30 day limit applies to the gamertag. You can change it on the website within two minutes after changing it from your Xbox with your gamertag. This will do the following:
A. Your Gamertag's WLID will be changed to that new e-mail.
B. All future Xbox Live and other Microsoft e-mails will be directed to that new e-mail.
C. You will sign into Bungie.net using the NEW e-mail address. Your old one never needs to be touched again.