Migration Issues between 2 laptops

The screen on my MacBook Pro cracked. My boss purchased a new desktop and gave me his laptop, which he cleaned off of all his stuff. Both machines are running 10.5.8.

To transfer everything, I initially tried to use Migration via Time Machine. I received an error about there not being a program to open the preferences file.

I then connected both laptops with Firewire, restarted the first (broken) one while holding T and then restarted the second (new) laptop. I selected my user and all settings/files/applications to be transferred. This operation completed overnight.

Issues:
On the new computer, my boss is still listed as a user. Migration simply added me as another one. He gave me his password, so I can log into his account, but I cannot get rid of it. Is this possible?

Time Machine is still not functional. I'm thinking he deleted something important when he was cleaning off the computer?!?!

System Preferences will NOT start for either user account.

I cannot view any Applications in Finder, though if I search for them by name they appear.

Two programs are missing - Safari and Preview. When I download Safari (using Firefox), I'm told that a newer version already exists and it will not install. I have no idea how to get Preview back. I'm thinking this is another thing he inadvertently wiped off the machine. Suggestions?

Is there a way to do a FULL system restore on the second laptop (new) in order to set myself as the sole user on the machine and fix all the missing files?