You can't accept OTA updates once you're rooted. Let me repeat. You cannot accep OTA updates once you're rooted. Not trying to sound like a jerk, but it's very important.
If you're absolutely intent on installing the OTA update, you must unroot first. Keep in mind that if you do, you will potentially lose root for a while. There are some ways to root after the OTA update (with 2.10 hboot), but they are not simple, and there are issues that come along with doing it. Let me put it this way. This is *not* a good idea.
So, that being said. What state are your phones in now? Did it just fail? If you turn the phone off, then press and hold the volume down button while turning the phone on to get into hboot, what do you see? Do you see anything from 0.97 - 2.02 version? Do you still have S-OFF? Once you boot up in android, is your rom still rooted correctly? If you answered yes to all, you're in good shape. If you have hboot 2.10, I'm afraid you got too far.
Here's what you need to do. Assuming you have full root and have not successfully installed the OTA update, make a nandroid backup of your current rom (as should be your normal practice), and flash one of these roms from recovery:
[ROM] RUU SuperSonic EvO 3.70.651.1 OTA - Stock - Sense - Deodexed & Odexed Version - xda-developers
http://forum.xda-developers.com/showthread.php?t=743781
These are basically stock, rooted versions of the OTA update to 3.70. If you do not know how to flash roms, follow the instructions here:
http://androidforums.com/evo-4g-all-things-root/194918-rooting-dummies-extras.html
Since the OTA included radio updates as well, you need to flash those too. You flash them from recovery like you do roms (but no need to wipe data). You can find the latest updates here:
[ Radios ][ 12-17 ] All EVO Radio, WiMAX, PRI, NV & HBoot versions - xda-developers
I highly recommend you make a backup using RA recovery instead of Clockwork before doing this, since it will make a backup of your wimax keys.
If you follow this process you will get everything need out of the new OTA (the rom and the radio updates). You will not get the new hboot, and there is absolutely no reason to ever update your hboot (at the moment).