First, are you completely clearing your browser cache? If you aren’t, you may be picking up some residual stuff when viewing the pages.
Secondly, try clearing the MODx site cache (in the manager, go to Site-->Clear Cache).
As much as I like deleting plugins I don’t use, i’d recommend just deactivating them for now, especially while you’re learning MODx. It’s possible that your homepage is still be altered by a plugin that you didn’t take out of commission completely.
I’d recommend that you get your site working with normal urls before trying to launch the friendly URLs. But there is this video about using friendly URLs when you’re ready:
http://www.youtube.com/watch?v=JlGiypZZTSw
Be really careful about hard-coding your urls! It’s a lot better to use the [~1~] type of tags to designate your links. E.g.
<a href="[~2~]">Squeaky's Show</a>
Do this even for your homepage, and you’ll cut down on the errors you get from links rendering incorrectly.
Just to double check... how did you go about deleting your plugins? Please share exactly what you did... it’s possible you missed something.
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