The EP values you use are irrelevant, as they aren't spent like cash. If you award 1000 EP per boss kill, people will be ordered the same as if you award 10. People like seeing big numbers, so I lean towards the former.
What is important is the relative amount of EP you give for different things: boss kills for farm vs progression, time spent raiding, bonuses for being on time or exceptional performance. Those need to make sense when viewed side-by-side.
As for GP values, you'd be very silly to use anything other than the values that the addon calculates for gear. It's a record of what was received, not something that you spent. If you used your own values, you'd have to re-calculate values for absolutely everything in the game, both now and in the future. You'd also have to make sure that you accounted for the slot modifiers so that the cost of a full set of tier gear + mainhand / offhand / ranged was the same for each class and spec.
10% decay sounds fine. Work out what the longest break you are comfortable with people taking before they are seriously penalized and figure out how many weeks your decay rate takes to get there. A 10% decay will take about 7 weeks to drop someone to half of their initial EP; 15% will take about 5 weeks to do the same. 20% does so in 3 weeks.
As for backups, I suggest you simply get a good backup program to back up your LUA files. You don't need EPGPweb to back things up - it's more to let people see their values outside of the game. I've never liked the idea of putting my data on someone else's systems. For backup of all my WoW UI (and the EP/GP values are backed up in the addon's saved variables files) I use a program called Cobian Backup:
It's free to use and automatically creates a zip of my UI every day, keeping 7 generations. Weekly, I copy the latest backup to an external HD. While I've lost a drive and sometimes screwed up my UI settings, I've never had to start from scratch since I started using the system. Get two regulars in the guild to do this and you shouldn't have to use EPGPweb unless you have a need to publish your member values to the web. I've never found it to be that important.
It does sound like in some ways you're getting caught up in the "EP and GP as cash" mindset that is common when coming over to EP/GP from a more traditional DKP system.
I wrote up an article on EP/GP a few months back that might be of some help to you:
The EP/GP Loot System « Cold Comfort
And a follow-on one about EP rewards:
It’s Raining EP – Cold Comfort « Cold Comfort
My loot policy showing the values I use may also be of some help:
As you can see, I use EP rewards scaled to the thousands. Hopefully that helps some; feel free to ask questions if you have them.