Dang that sucks you've gone through 2 motors but I'm sure you'll be happy with your new LS1!!
I am not familiar with the Atomic LS kit you mentioned so I just googled it and does look like a pretty trick setup! Personally because I opted to go with a crate motor which comes with all of the fuel rails etc. I didn't really look into aftermarket ECU setups mainly because factory stuff almost always works best
Plus with 480hp I'm not that concerned about needing more right now!
I must say though, you don't get the tune-ability with the factory setup as you do with the Atomic setup... but the factory ECU/harness kit only set me back about $1100 and I'm pretty sure I can buy tuning software for about $600, or just pay a known local tuner to dyno tune it for the same price, just don't own any software then but I'm fine with that~ If I was building a motor from a used unit I'd probably use the Atomic setup just to get the new fuel system components too... Then again that is why I opted for a whole new engine because I didn't want anything to go wrong that I had to pull the motor back out for!
Start a post on your build, I'd love to check it out! If you have any questions feel free to give me a shout!
Good luck
J