Ok that helps allot mate.
I'll do as you suggested and go a clean update and try the whole process again cheers.
I'm going to use a different E3 update.
I think my problem may have been using the latest E3 firmware here: 2012-01-05 E3 flasher upgrade file download, support fast dual boot. Please note if your console can't dual boot, don't upgrade this firmware. <<--- (It actually told me if I wasn't dual booting not to use it lol I just blatantly went for the *latest* firmware.)
Instead of:
2011-11-22 E3 flasher upgrade file download, support backup bios 3 times automatically.
Can someone confirm this? My ps3 probably can't dual boot (CECHH) so I should be using the 2011 copy shouldn't I?
I'm going to go try this and will get back to you all with the results. Thanks for the help so far

great community
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Hmm ok I actually managed to get to the "connect controller with usb" screen this time.
Re-updating the firmware did it thank you.
It's just one problem after another for me atm lol Now my dongle is not working. I'm using PS3Jig. Some people have had success with it and others not so much.
PS3Jig does the whole process challenge accepted, challenge received and Done! but the PS3 does not turn off by itself like it should. After about half an hour of waiting for it to turn off I switched it off at the back of the PS3. When I turn the PS3 back on it is the same "connect controller with USB screen". Does anyone have any ideas on this?
I have a HTC Desire HD android phone and I'm going to try track down the program Klutsh made just like PS3Jig (psfService Mod). I'll get back to you all on how this goes.
Cheers