Did you ever figure this out? I've been through the same thing with my N2 and eventually have scavenged together 1 rock solid one (touch wood).
"Boot failed..." comes up because the bios linux kernel was unable to load aeinitrd and aevmlinuz, normally caused by a dead hard drive. I'd have to take another look at the script it runs and what exactly causes boot failed but it's something along those lines.
In terms of the one that freezes, the MSI based boards used do tend to have caps go bad, check if any are bulging. The warnings that come up during boot is normal, it's the game setting up its work mounts (stores bookkeeping, leaderboards etc). After it goes back to the namco logo for a little bit and the screen goes back, this is when the game executable is launched.
Mine has been partially recapped with nichicons, but now the ones that weren't replaced are starting to go too.
I would troubleshoot the one that's freezing with a new power supply first, it's all standard atx so anything around 300w up should be fine, as well as check for suspect looking caps. Could also chuck some replacement ram at it (I had a stick randomly die on me in my test bed N2 I'm using for research on the boot process)
