I was having the same issue your having trying to flash VirginMik Rom, Newts One S Rom based off the LTE phone dropping soon, and ViperRom IC3D. I learned when your flashing these newer ICS ROMS, (I was only able to use Mean Rom as well), the Recoverys are not able to flash "custom kernels" needed for these ICS Roms. So this is what I ended up doing. Everywhere I looked I kept reading the Flash Image GUI is the answer to flash Kernel without using recovery. My issue was I couldnt make it past the boot screen to flash anything. So this is what I did to flash the roms I listed. Dont know about the others but this is what worked.
Find AnthraX-htcleak-rls1.zip and put it in the root of your SD card.
Get 4EXT Recovery Control, (free version works. I heard. But I wanted to make sure I had the "Smart Flash" option for phones that have S-On)
https://play.google.com/store/apps/details?id=ext.recovery.control&hl=en
Download Flash Image GUI
https://play.google.com/store/apps/details?id=com.joeykrim.flashimagegui&hl=en
Make sure you have the ROM of choice on your SD card of course. If your using Mean Rom and its stable it may be a good idea to start from that ROM. Also backup your Flash Image GUI and 4EXT Recovery Control to your Titanium Backup.
Open your 4EXT Recovery application. It will ask for you to update and such to install the recovery on your phone. Once its installed. Try going to Recovery just to make sure its installed on phone. If it is, you should be ready to move forward.
Wipe the usual (data, cache, dalvik cache). They have an option to wipe everything but card using this recovery. Go to tools and make sure "Smart Flash" is enabled. Flash your ROM of choice. After you flash your rom. Use the "wipe Cache+Dalvik Cache" wipe. Then flash Chads Anthrax AnthraX-htcleak-rls1.zip Kernel. (The reason your flashing this is to be able to get past the Boot Screens on these ICS roms).
Once you make it past boot screen and log in to your Google Play account. 1st thing you should do is Install is the Flash Image GUI app. Use this
How to Install Kernel/ROM without Fastboot on HTC Evo 3D HBOOT 1.50 Using Flash Image GUI App! - YouTube
if your not sure how to use this app. Once you flash the correct kernel this app will be extracted from your current ROM being used and your ROM should be stable after you reboot. The Anthrax Kernel seemed to make my phone reboot randomly on certain ROMs after a while. However it helps me get past the boot screens. I've also tried this Anthrax_ICS-RLS5.zip but didnt really see a difference. I dont believe they are made for the ROMS I named but do what they need to get past boot screen.
Again..This is what worked for ME so I wanted to share. Not liable for any bricking and etc. I was going nuts for about 2 weeks before I figured this out. Life was much easier on Boot 1.4 before I had to get another and ended up with Hboot 1.5. However these 2 apps brought me back to what it was like flashing ROMS without fastboot. Even slowed down my decision to wanting to get the New LTE...
Hope this helps you