I have been considering for a long time rooting my phone, for better performance, overclocking, etc. but have been a bit hesitant to do it.
The extended battery is great. It's 1860 mAh, and ever so slightly thicker than the stock battery - I actually prefer it because the added thickness (maybe 3mm or so) makes the phone a little more comfortable to hold in your hand... but just a preference. If you decide to get one, make sure it's a legit Moto battery (part #BP7X) - I've heard tales of problems with some of the cheaper knock-offs.
Rooting your phone is pretty easy- some of the apps only take one or two touches to root. Generally speaking it isn't rooting that causes the problems, it's what you do after the root. Don't go crazy with some of the apps that are readily available, just use some of the simple ones that you understand.
If you decide to root go to My Battery Life Writeup in the D2G forums here on this board. It tells you some of the stock apps (AKA battery suckers!) you can freeze that come on the phone with Titanium Backup. Freeze them maybe 1 or 2 at a time so you will know how to reverse if there are problems. Get the stock like you want it, then use TitBu to backup all of your apps. Then, in a disaster, you can reinstall them all without having to download them from the Market again. The key- just don't go crazy after rooting!
As for batteries, may I recommend the Gorilla Gadgets Extended Battery? It is twice the size (3500mA I believe) and is great in these phones. I have had one for several months now and I don't think I could live without it. I can go all day on it, with plenty of juice left at the end of the day.
Don't give up! Keep trying different arrangements on your phone until you get it to a point you can live with.