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Hope you get it fixed man,

Might be a bad SATA connector which is making both hard drives look bad. IDK exactly tho.

What happens if you just try to start it normally does it say :Hard disk is corrupted: Not sure if this will help even to the slightest haha. But a long time ago i had a ps3 where there wasnt enough pressure on the GPU and the motherboard had actually been taken from a seperate ps3 to that one. I would start it up and it would turn on perfectly fine but would stay in black screen until it said one of two things. :Hard disk is corrupted: And i'm not sure the second error it gave. Either way. Moving on i actually ended up stacking some pennies onto the GPU in the motherboard to give move pressure to that spot. Being the motherboard has been swapped from a 60 GB and put into an 80 or vice versa it didn't put enough pressure and the ps3 wouldn't read anything correctly. I covered the pennies in thermal paste. This is no joke by the way. Used pennies because they are copper. Covered the pennies in thermal paste put four of them onto the GPU and started it. To be honest if you have it taken apart i couldn't see the hurt in trying it :O. IT worked perfect and still works to this day. I know it sounds a little off the charts but that's what i did to fix my problem thought i'd give my imput

Well, i have an E3 flasher (not hooked up to it) so if i take the sata cord from that can i use that for a temporary thing to see if that is what is wrong?

Make sure sata connectors are connected from both ends. This happens when dissembling of the PS3 happens and it comes unclipped or lose. Should fix the problem

Also, you might want to try putting the HDD into a different PS3 and formatting it. Then put it back in the CFW one and reinstall FW.

Dont think that is it, i can hear the HDD spin up when the ps3 boots

Have you installed the Original Firmware again with the new HDD??
You must do this. To get it into a readable PS3 Format. Formatting to FAT32 on PC will not work.
Hope it helps!

sorry but wrong section