Hello,
First off, I apologise for being a noob. I've read hundreds of forums and webpages about rooting, ROMs, nand locks, HTC Desire, and for all of it, alot of the 'basics' are still... unfamiliar to me. I've tried to understand it, but it hasn't been dumbed down enough for me, so apologies in advance.
That being said... I used unrevoked on my desire, and hooray! it worked. Superuser was installed, clockworkmod was working, all was good. I tried to remove a few of the lame htc apps from /system/apps (first thing I did heh) but whenever I rebooted, there they were again! Eventually figured out it was read-only, changed to read-write, but same problem. After research, it seems S-ON is the cause, but I'm fine with overlooking that for the moment. What's strange is that somehow I've deleted google maps from my phone. It's not in my apps list. However, there is a Maps.apk in /system/apps (but no .odex file for some reason) and attempts to delete it, install it from that location, install from market, install from a separate package, all fail. Even using pm via adb gives me "invalid_install_location" error messages. So I'm assuming that somewhere, android is still listing it as a System app, but isn't finding it in /system/apps? Could anyone give an opinion on what's gone wrong?
I made a backup using nandroid when I first got root, and have restored the /system partition, but no luck.
Other things that are weird - performance seems slow - lag spikes in keyboard input, settings not being saved (this so far applies to my keyboard, and superuser privileges which is quite annoying to authorise everything dozens of times a day, and yes, the Remember flag is ticked). Scrolling the home screen seems sluggish, and when adding apps/widgets to a screen, the highlighted section doesn't match up with where my finger is. I can't put an app on the right hand side column, because it keeps using the second-to-right-hand side column, and if I go further with my finger, the screen scrolls. Weird huh? Related to the above, I can't make a hosts file in /etc (or /system/etc) so AdBlock doesn't work

I could unroot, I think. Would this restore everything to how it was (including the missing apps and performance) ? I could try AlphaRev and mess around more with my /system. I could try a custom ROM and do a "clean" reinstall after wiping everything. Is there anything else?
On that note, where are things like contacts, SMS messages, accounts, etc stored? Is there a way to backup just these items so that I can reinstall them after a wipe/reinstall, and then add apps one at a time?
Advice, theories, help, and dumbed-down explanations of this whole process for the noob, all would be greatly appreciated.
Thank you for reading.