Sorry for the delay. This is a lot to read, but hopefully it will be informative and useful.
User preferences from your backup, for the various applications, should be stored in your home folder's Library/Preferences/ (/Users/jennie/Library/Preferences).
In the case of Freehand, you might find a Macromedia folder there, and/or com.macromedia.freehand.plist (could be named something slightly different...)
Copy any that seem appropriate, for each app that you use.
Bear in mind that preference corruption may have had a hand in causing slow performance, so move a few prefs, test, log out, log in, test, then move a few more... It's sorta painful, and definately tedious, but it's really the only way to proceed when you can't be sure what was causing the problem in the first place, and have a bunch of application preferences you want to keep.
If in this process you log out, then log back in, and things start getting sluggish, then the culprit is likely a preference you just moved.
There is probably a higher level issue with access privilege settings for applications and /Library/Support items with regard to Freehand (but potentially other third party apps you copied).
Cause: When you copy files in the finder (drag and drop) from an external drive to your internal, you are copying the files with your user accounts privileges. Applications generally expect to be set to owner=root, group=admin.
After the copy operation under your account's privileges, the applications are probably set to owner=jennie, group=admin.
Result: Some apps will request authorization to run, expecting root authorization. Freehand seems to be having this problem.
Solution: This can be resolved pretty quickly by issuing the following command in the terminal:
sudo chown -R root:admin /Applications/*
You can copy and paste that sudo command into the terminal.
Type your user account password (should work fine if your account is an admin account). It should take about a minute, maybe less, maybe more
My applications folder weighs in at just over 5 Gigabytes, and it took about a minute to complete the same operation.
NOTE: Some applications do not seem to care who owns them, probably becuase they don't need to change/access anything at a high enough level to require root privileges.
Let me know if you need additional info and/or clarification.