upgrading versions definitely keeps your configuration intact. Still always a good idea to do a backup prior to any upgrade, but you should be ok. There are thousdands of systems alread on 13.
I would caution you on running any outside scripts unless you fully understand what they do. One of many motivating factors of the introdcution of the firewall module was because of the vast amount of carnage we've seen from people running outside scritps that they don't understand. More often then not, you find most of such scripts are not aware of what FreePBX or other aspects of the system is doing and they are usually much more likely to create problems.
Again, if you fully understnad them, and are quite versed in FreePBX and internals, you may be ok but given your questions, I'm guessing that may not be quite your comfort zone?