I like Eclipse as well, but I had one major issue with it: bootlooping after clearing the Dalvik-cache (I mess with the optimize/verify settings a lot). So, I went back to stock rooted, ZipAligned all of my apps, and did some SQLite database cleaning (the scripts are part of V6 Supercharger, which make that easy). I've also modified my touchpad.cfg to accept 10 touches, though 5 is the usable maximum. I also did a few modifications to increase accuracy and sensitivity, which I'm still testing.
(DO NOT edit the touchpad.cfg with ES File Explorer as it converts the file to another text type and will render the touchscreen unresponsive; I don't know how many times I had to manually push a backup of touchpad.cfg to the phone via the ADB shell; instead, use Jota Text Editor and copy it with ES File Explorer [or by using shell commands]).