2011 MBP slow and won't complete backup

Hi all -
I have a 17" 2011 MBP, 750GB HD, 8G RAM, pretty hefty machine. Os10.8 Recently it's been generally slow. It will not complete time machine backups, and often takes many minutes to reboot. Sometimes I have to kill the reboot with the power switch and turn back on manually. Occasionally programs take a long time to open, and sometimes they show open on the dock but no window pops up. In this case I have to kill the program with forge quit, and reopen. This usually solves it, but not always.
I took it to the genius bar, as it is still under applecare for another month from the previous owner, and the decided to replace the hard drive. Picked it up yesterday, restored to my most recent backup, Nov 11, 2012, and started installing a few small software items that I had purchased since the latest backup, mostly AU plugins for Logic 9 and MacKeeper 2012.
The problems persist: very slow reboot, slow performance, and not able to complete backups. I had read that mackeeper can slow down one's system, so I uninstalled that by dragging the icon from the applications folder to the trash, initiating the uninstaller. That didn't seem to change anything...
My backup scheme is a little unconventional: I'm not using time capsule, rather an airport with an external g-tech 2GB drive. It worked fine up until recently.
Any ideas? Something is definitely wrong, but what I have no idea. I have another genius appoinment next week, but if I can solve it on my own, I'd rather do that. Given the last misdiagnoisis, I'm not sure if they are the best for figuring this stuff out or not.
Anyone have any ideas?
Thanks!
Geoff

Had an appointment at the genius bar this weekend and he cleared up several things for me - reset some permissions amd generally cleaned up a few things that made the machine run much better.
Notably, I had an external FW drive that I use to store audio files and logic projects, which I had ignorantly told time machie to back up when it was connected. the genius guy said that if i do this it must be connected EVERY TIME time machine backs up, or it will screw up the system.
Short story is that I repartitioned my backup drive, backup up hard wire via FW800, and all seems well. The computer is back to normal operation seemingly.
He also recommended exlcuding a couple of things from backups, notably the stuff related to the parallels desktop, which leads to my first new question. I did the first backup without excluding anything. Can i now exclude the parallels directories from subsequent backups without messing things up?
And the second, more general question: best way to automatically back up a portable external HD that may or may not be regularly plugged into my system. Is there a way to do this automatically or must it be manual backups only?
Thanks so much!

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