if you insert a new ms, you don't need to reinstall the lcfw, not if you reset the device.
install plugins by putting the .prx file in the in the 'seplugins' folder and registering it on the texts files (pops, game, vsh, etc.) ie cxmb plugin should be "ms0:/seplugins/cxmb.prx 1" on the vsh.txt.]
i think, if you're not familiar with the vsh menu entirely, you shouldn't be tweaking it alot. you're more likely ending up having issues about black screen or the menus not showing up.
for running iso, you're good as long as you have a cfw/lcfw installed. no need to configure something else up to run the back up.