Migration problem with TM

Just bought a new iMac and migrated over everything from my old G5 iMac. When I came to use TM on new iMac it says my ext. HD only has a few GB left and can't use it. How can I get the new iMac to recognise all my backed-up files from previous G5 Mac (and now migrated over to new iMac) and continuing backing up via TM on the iMac as before?

I thought TM could do this too. But in my case TM created a new folder even though the Computer Name was the same (migrating from older Intel iMac with OS X 10.5.6 to newer Intel iMac with OS X 10.5.4). IIRC it just added an extension to the folder name.
If only Apple informed customers of these details, and others, with migration and using TM instead of making it out as though all you need to do is hook it up and go. There are things to consider before proceeding, which in my naivety I assumed Migration Assistant would take care of (doesn't it know it's migrating between two different HW iMac's and not to transfer system files that may cause a conflict?). Now my new iMac is infested with my old iMac's files, hindering it's performance. And I've already created new backups of both TM and SuperDuper! In hindsight, I should have not migrated (transfered files) right away with the set up assistant and instead updated OS X on the new iMac and then transfer only user files and reinstall apps (which I thought I could avoid with MA). Sadly, I'll be doing a fresh erase/install of OS X now, copying only users files over this time from TM backup, and then reinstalling apps since my new iMac doesn't seem to be operating smoothly.

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    <Jun 3, 2010 1:14:57 PM MDT> <Notice> <LoggingService> <BEA-320400> <The log file C:\Documents and Settings\tosbor001\Application Data\JDeveloper\system11.1.1.2.36.55.36\DefaultDomain\servers\DefaultServer\logs\DefaultDomain.log will be rotated. Reopen the log file if tailing has stopped. This can happen on some platforms like Windows.>
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    <Jun 3, 2010 1:15:25 PM MDT> <Warning> <Deployer> <BEA-149004> <Failures were detected while initiating deploy task for application 'tamjhssec'.>
    <Jun 3, 2010 1:15:25 PM MDT> <Warning> <Deployer> <BEA-149078> <Stack trace for message 149004
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