Data Migration partially failed - try again?

Hi, I used the Data Migration Assistant tool to transfer all data from old MBP (OSX 10.6.8) to New MPB Lion. UNfortunately it hasn't seemed to copy over all data or settings sufficiently. After a bit of searching around this may have been because I had not upgraded the Data Migration tool on the old machine.

My question is if I do another transfer now will it copy everything over again and cause problems / duplicates of the apps etc that it has already copied or will it replace. I have attempted a re-install of Lion on the new machine as I thought this would restore to factory settings but not so, and this probably wasn't the right thing to do... Any advice is much appreciated!

 

Urrrgh it everything seems to be greyed out / un-selectable under Disk Utility > Partition, plus makes me very nervous on my brand new machine :|

Can I definitely just not do another data migration over the top?

 

Ah ok, when accessing Disk Utlility using CMD R I can erase. Do I erase the 500.11GB TOSHIBA MK disk or just the partitioned Macintosh HD?