Guys, there's a simple solution to all this while the download links are AWOL.
I realize I'm preaching to the choir, but for the most part, FAKKU is an aggregator site - it's grabbing the manga from other translator sites and centralizing them. (In many cases those other translator sites have been posting their manga here as well.)
There's nothing wrong with loading each chapter in the viewer and downloading each page separately, but you're doing things the HARD way if this is your primary method. (You also run the risk of the viewer down-scaling the resolution of the pictures to speed up the loading times. MOST web viewers do this by default, by the way.)
The point you all seem to be missing is that the original translator sites still exist - and still offer download links on their own pages (for the most part.) On EVERY SINGLE chapter/story listed on FAKKU the translator is listed. Google the translator and you'll find their site; search the site and you'll find the item you're looking for.
And if THAT doesn't work, try a generic Google search for the name of the title. For example try the string "If We Could Meet By the Sea mediafire" and you'll find half a dozen links to that particular file, hosted on file aggregators like Mediafire, FilesTube, RapidLibrary, etc. I've often used this technique when the original hosting page has had its file links nuked.
And if you don't know how to use Google's advanced search features, now would be a GREAT time to learn! Type in your search string, the click the GEAR button in the upper right of the search page for more options. (This is INCREDIBLY useful when a site doesn't have a tagging feature implemented, since it allows you to search deep inside the site directly from Google.)
More options: If you don't want to have a bazillion file download windows open, or hate keeping track of them, then Try JDownloader:
HOMEPAGE - http://jdownloader.org/
Once you've got it installed and configured, you can simply copy your download links and the program will throw them into the DL queue, then prompt you with a Captcha Popup from the site when it's ready. This is an incredibly powerful program - learn how to use it and simplify your life. Do yourself a favor and make sure you're only trying to grab 1 file/site at a time, unless you've got a premium account.
Alternately, you can also use a site's RSS feeds and tell most Torrent programs to watch for new files to become available. If you've got a series you absolutely love, then using this method ensures that you know when the next chapters are coming out. That way you don't have to remind yourself to go grab the file - just leave your torrent client running, and it does the babysitting for you!
Is this a little less convenient than having the Download links compiled for us on FAKKU? Absolutely. We're all grateful that Jacob and his crew do so much to bring us our daily fix, and it sucks when things aren't working precisely as we want, or are used to. But when it comes right down to it, he doesn't owe us anything. It's his web site, and if he needs to take certain functions offline while he re-works the code to make improvements, then it's his choice to make.
Hope all this helps, guys. Good luck, and happy fapping.