Things to consider.
Previous to 10.4 OS X was not very good at self maintenance. Long boot-times are indicative of any or all of the following:
1. Permissions in need of fixing.
2. Disk or directory dammage.
3. System level maintenance still outstanding.
4. secondary device/volume with any of the above issues present in such a manner that they are relevant to the booting system in question.
Troubleshooting proceedure:
(Note: If your HDD is in poor shape physically or your directories are dammaged beyond the point that Disk Utility can recover, any of these proceedures may push your system over the edge... Then again, so would nearly any use of your machine, beyond a certain point it becomes roulette)
1: Restart or cold boot holding down the shift key. THis forces your Mac into a self-diagnostic mode. Continue to hold the shift key until you get a "safe-boot" login. This may take a VERY long time so think about wedging or taping the key down (you may want to practice with the machine off). This proceedure will run a permissions fix and eventually a disk diagnostic/repair. Once you're in "safe boot" go ahead and restart again.
2: "Get Info" on the boot disk and run a fresh indexing. This also will take some time so you can geton with #3 while it's running.
3: Open the Terminal and type the following precisely:
sudo sh /etc/daily/
*the system will propt you for an admin password, enter it and hit return, it will not display what you type so don't be phased when it doesn't.*
when the operation finnishes follow up with:
sudo sh /etc/monthly/
and finally (takes the longest):
sudo sh /etc/weekly/
These actions clear out a number of OS level caches that can get overfull if your machine doesn't run for extended periods idle and NOT asleep, particularly if it does not sit idle over night.
4. Open your User control pane in System Prefs and shut off any login items.
If none of this helps you may well need Disk Warrior or one of Alofts excellent disk tools, you may also benefit from a restore-install.
Things to know about the future:
Even though Migration is technically supported from OS 10.2.8 upwards the Intel machines do not reliably interface with User Accounts present in pre-OS 10.4 systems. I migrate data several times a week for customers and the older your OS is the less reliable migration becomes. Some have speculated that this is due to hardware limitations of older FW machines but my experiences suggest it is more directly linked to the generation of the OS present in the previous system.
Good luck!