The block chain hasn't finished syncing after about five hours now, and I made no alterations yet to the genesis parameters or the nxt.properties (although while it is syncing I've added the nxt.addOns=nxt.addons.JPLSnapshot statement but obviously the blockchain is just going through the motions in the background and I have not yet added that statement to the current active version, I guess I will have to restart the process for it to take notice and incorporate the line in the nxt.properties file where it was added? I suppose I should wait for the blockchain to sync (are my suppositions well-guided?), and then, activate the added nxt.addOns=nxt.addons.JPLSnapshot line in nxt.properties, and THAT will make the browser-accessible gui finallly appear and display itself and all its vital functionality. Also is ther someone who can guide me through this who has enough patience for an apprentice level n00b with a high level of curiously but little scope of this. Like, could I also set transaction fees for the currency / blockchain. Where? Maybe it is in the GUI but as I mentiond I haven't gotten to the GUY but at least everything is just barely now almost leading up to it being properly functional.
If you are syncing the blockchain from scratch it will surely take several hours to do so. Just check the logs or open the wallet to see the progress.
Your understanding about the configuration file is correct: it's read upon the node start so any change after that will not be picked up until you restart the node.
Finally, about cloning the blockchain, if you want to change internal parameters you will need a good understanding of Java and spend some time reading the code. There are really no shortcuts there.