Lion won't boot (difficult upgrade with relocated home folder)

i seem to be having a very difficult upgrade and am hoping for some more help.
i have a 2006 mac pro with LION on the drive in bay 1, a partition of windows 7 on drive 1 and my HOME FOLDER on the drive in bay 3. i also have a drive in disk 2 which contains a CLONE of the OS on drive disk 3 started reporting a need to Repair when running DU - and this Repair ran into complications - so i just decided to upgrade to a new 2012 computer and move along.
right now i have all my data and yosemite on the new 2012.
/however/ my TIME MACHINE drive will not mount on the new computer and even when i try to force it to mound (right click on the drive in DU) it will not mount and asks if i want to initialize it.
so i tried to boot into the 2006 computer with LION in order to see if i can get the TIME MACHINE drive to mount and no i enter my password and now this computer won't boot and i am getting a cannot boot error of some kind (this happens after i enter my password). i have /also/ tried this with my external CLONE of the OS drive in bay 1 and i also get this error.
so here are my questions:
1. i moved some data around on the HOME FOLDER disk in drive 3 and i am wondering if possibly this is the issue. also, this drive was reporting as needing repair and has still not been repaired. can i remove this disk, put it in the new computer, REFORMAT it and then CLONE my external backup of this drive back to this drive - and then place it back in the old machine and see if this works?
2. can i take the drive in bay 2 that has the CLONE of my OS drive in bay 1 and put it in bay 1 and try and boot into LION off this drive?
i would like to keep LION running in part because i have a couple of boot camp installations (one i would like to migrate over to the new machine) but also because i want to see if i can still have access to the Time Machine backup.
thanks for any help as i'd like to get unstuck a bit here.

All the various boot key combinatiuons should be pressed immediately after your hear the boot chime.

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