First issue: you didn't tick the box to add MySQL to your PATH.
1. Find where your mysql.exe is, and copy the location from windows explorer (mine is in "C:\Program Files\MySQL\MySQL Server 5.7\bin"
2. Right click on "Computer" then select properties (I'm assuming you are using Win7).
3. Click on "Advanced System Settings" on the left
4. Click on "Environment Variables"
5. Under System variables, find "Path", click on it and select edit.
6. At the end of the variable value add a ; then paste the path you copied earlier.
7. Click on OK twice.
8. Now either log out or reboot (may as well reboot).
Second issue:
I had this problem too. It looks like the peq daily database actually misses a ton of the scripts needed to set up the eqemu database. What I did was get the old link (that says don't use this database!) and copied all the player scripts etc, then sourced those. Not sure why the required SQL tables aren't included in the source code.
I'm also a newbie so hopefully someone will fill us in
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