Minecraft Server ??S

I have a dedicated PinguyOS box for a Minecraft Bukkit server. It ran fine for about three weeks until an internet outage. When the internet signal was restored, the server couldn't dither the login names with the big MC Auth server and noone could log in. (yes I had port forwarded and yes the server was open to the internet but only one outside source was logged in and they are trustworthy)

Here comes the Pinguy issue...
After tens of hours scouring forum, as we do, I found a reluctant solution, switch the server.properties file to online=false and viola, we all could log in again. It was at that point that I no longer could connect to web pages with a browser which didn't stink too badly, but it came around to update time for minecraft.server and my copy of McMyAdmin to run the server. Since the machine couldn't connect to the internet, the MCMA is now stuck in a "do you want to download this update? Y/N?" state and my .jar file for the MC server is gone. Cant d/l a new jar file for the server nor run the update to MCMA.
I have posted to their forums and am not as certain of their expertise as I am this forum's because face it, you guys just know more than them and I always get the right answers here.
Please help, and I'm not beyond remote desktop control for resolving whatever is the issue.