The version I've been using is a dragino HE on a custom board
The firmware is Dragino-v2 common-2.0.7
http://wiki.dragino.com/index.php?title=Yun_Firmware_Change_Log
It looks like there is now a newer firmware from the beginning of this year. I might give that a shot.. it looks like it has a newer version of CPU-MCU-bridge. I'm not sure if bridge is what is hanging up. When I do a reset-mcu command it appears to put everything on track for a couple weeks. Uptime is important in my application and the Linux side of things has chugged along for several months (when I last reset power). It's weird to me that it appears I'm having trouble with uptime on the MCU. Is there a changelog for bridge? It looks like the one on my install is only 1.6.0.
I believe the web files are stored on the sd card. I don't think I have a log or any other files that would eventually use up all the memory.