Have you considered the possibility of starting a new website from the ground up and "freezing" the old website? That way you can keep all of the old stories nice and safe while taking in new stories through the new website in a new, singular shared archive/table/whatever. This way you won't have to worry about manually porting anything until much, much later.
I understand money is tight, but you have a dedicated community. I'm sure with some thought you can find SOME solution that won't require you to "live with what you got."
I keep reading announcments from as recently as this month on the front page about how the community is growing. Here in the forums I keep reading that you're struggling to keep this thing afloat. This is sending mixed messages.
It sounds a lot like you are working with an outsourced server with all the talk of data limits and hosting costs. Have you considered the possibility of hosting your own server? Terabyte hard drives are not that expensive anymore, and since fanfiction.org is a text-based site, bandwidth is a lot cheaper. I've seen simple servers that go for as little as 400USD (software not included, but linux can get you stuff for free). As a server owner, you would have more control over what you CAN do as opposed to what you are forced to do.
Again, you have a dedicated community and you would have to crunch the numbers yourself because I have no idea what things would cost where you live. You know your local companies better than I do. With websites like kickstarter, you could potentially fund a professional upgrade of everything including software. By professional, I mean hire a contractor to do the heavy lifting.
1000 people donating 10 dollars each will get you $10,000.
If those numbers on your front page are not just for show, that is. I'm trying to help, here. Running a website isn't easy, I know. However, the problems you are running into right now sounds like a chronic problem that won't go away without a major change in something fundamental.
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As for Bronx, I'm one of those users that actually read all of the FAQs before posting as well as all the TOS and User Guidelines. The fact that I know as much as I do about this website comes from what YOU guys have posted and what I have seen. Your hostility is unhelpful. I reccomend YOU read the stuff YOU write before accusing others of not doing their homework. The one thing I hate more than a broken website is when the staff get hostile when someone points out a problem. It is unprofessional and most of all wrong.
The only reason why I KNOW how to submit stories is because I spent an hour SEARCHING for the FAQ.
The user interface is a mess, and new users struggle to figure it out. That much is obvious.
A broken user interface is the number 1 reason why websites fail.
"I know where everything is because I've been here since forever" is NOT a legitimate excuse. If anything, its a sign that the website is in decline when the community and staff say that. Turning away new users because you don't want them in your 'sekrit klub' never works. If anything, it HURTS ad income. You want more hits and clicks, and the only way to do that is new users.
Accesibility should always be your number 1 priority.