Somethings gone horribly wrong: Installing new ROM wreaks havok

[Sileem]

UPDATE:All fixed, I flashed back to stock, rerooted, and now everything works as it should!

I have no idea what's happening or why it's happening, but attempting to install a new ROM just goes horribly wrong.
Right now I'm running BB with Franco's Kernel M1. I tried doing a fresh install:
I wiped Data and Cache, then installed the Kernel, boot back into Android, first thing I get is the "Android is Updating" window, I let that finish, and now it skips over the first time initialization, weird. Next I notice it is incredibly laggy, I figure this was because of a fresh ROM. I look in Apps and it lists all the apps I had install previously are still there, wtf. It shows the grey android icon next to it, I have no idea why they're there. The Home button did nothing and there was no lock screen.
I guessed there was something wrong with BB, do I tried the same with AOKP, same results. Does anyone know why this is happening? Something is really wrong.

 

[Droid-Xer]

Which recovery are you using? And did you also install gapps?

 

[Sileem]

Which recovery are you using? And did you also install gapps?

Tried with the unofficial CWMR Touch Enabled (Beta 5), I'm trying it again right now with the official CWMR (no touch) 5.5.0.4.
I installed gapps with AOKP, I don't think they're necessary for BB
EDIT: CWMR didn't change anything.

 

[Droid-Xer]

You're right I think bb has gapps included. Ya try a different recovery and also ensure you're downloading toro builds for the Verizon nexus or magoro builds for the GSM nexus.

 

[Sileem]

You're right I think bb has gapps included. Ya try a different recovery and also ensure you're downloading toro builds for the Verizon nexus or magoro builds for the GSM nexus.

I definitely have the toro builds. what other recovery can I try? Also, is it possible to install roms through ADB or fastboot? Or even format the partitions?

 

[Droid-Xer]

No flashing through adb. Just use the official free clockwork through rom manager. Probably also check md5 sum to ensure you're getting a proper download.

 

[Sileem]

No flashing through adb. Just use the official free clockwork through rom manager. Probably also check md5 sum to ensure you're getting a proper download.

Tried with the official CWMR, same results, MD5 matched on AOKP, I can't find where Pete has his MD5sums, but I'll assume this isn't the issue. I might relock and get a replacement from verizon.

 

[Droid-Xer]

So you're just flashing the rom and gapps right?

 

[Sileem]

So you're just flashing the rom and gapps right?

I've tried AOKP + gapps
AOKP + gapps + Francos M1
BB
BB + franco's

All of these combinations yielded the same results

 

[Droid-Xer]

And you're doing a factory reset prior to install? That's odd. Not sure what the issue could be.

 

[Sileem]

And you're doing a factory reset prior to install? That's odd. Not sure what the issue could be.

I've tried Factory Reset and wiping the partitions from the partitions menu. I just flashed stock, I'll try rooting again, if that doesn't work, I'll just go to verizon and get a replacement. 4 and a half years of paying insurance might finally pay off.
UPDATE:Flashed Stock and rerooted, now everything works!

 

[Droid-Xer]

Great!!