After unlocking the phone I /would not/ recommend using RSD to flash /anything/.
When you unlock your phone, you burn a bit fuse that tells the phone you've unlocked it. There is no way to undo that. Using RSD improperly can cause your phone to hard brick and render it useless.
To avoid possibly breaking your phone from this point I would recommend taking a close look at what ROMs are available in the development section to see which one(s) suit your needs. Listed below are the ones I use on any of my three Motorola Atrix 4G's ( US ATT )
Neutrino ( CyanogenMod 7 Base )
NottachTrix ( Closest Stock Experience IMO and more customizable )
Currently I run NottachTrix because I like webtop, but prior to getting a lapdock for this phone I ran solely on Neutrino EE with 0 issues.
You'll want to take a look at setting up Motorola's USB drivers
for ADB / Fastboot usage these are a must.
For either ROM to flash properly, AFAIK, you'll need to use ROMRacers Recovery found here.
These are just my personal favorites, as there are a plethora more ROMs out there in the development section. There may be a stock ROM that I just am not aware of you can flash through recovery, but I wouldn't know off the top of my head.
As far as fixing the boot-loop issue goes I would go into recovery and wipe cache / data / dalvik cache, under advanced in recovery, and then reflash the ROM you're trying to use.