Yes - you can uninstall any program including backup managers or ftp and install it again. Please note that some backup managers keep backups under their install folder so by removing it you'll delete all the backed games as well.
Yes - you can reformat the entire hard drive and yes you'd need to have the (3.41) firmware ready on USB stick and it will accept it so no need to install higher / latest FW.
Indeed - do NOT install any FW updates from the game disks - you can as a precaution even delete the UPDATE folder and / or UPDATE.PUP file from you backed games.
And yes - you can install any game updates - but it not always works as smoothly so have a look around our forums and have a bit of read what eventual issues you might be facing as well as possibility of being spotted by Sony using JB-en PS3.