Not an expert, hope this helps:
1) Leafpad: have to open scmapps (either through the icon in wbar or right-click on desktop -> System Tools -> Scm Apps. Click the button Apps (upper-left corner) -> local -> install should populate the left-side panel with the downloaded scm. Highlight leafpad and click the button Go at the bottom -> it should run now
2) As for leafpad, no idea. As for abiword, as it is a tcz, it should be "on demand". Right click on desktop -> System Tools -> Apps. Click the button Apps (upper-left corner) -> Maintenance -> On demand maintenance. That should populate the left side panel with the tcz you have, click on abiword.tcz -> it should go to the right side panel. "Current OnDemand Items". From now on when you right-click on the desktop, you'll have a On Demand section, clicking it will show you "abiword" and clickin it should launch it
3) What I have is persistent home, opt and tce (as I use it fom a pendrive:
APPEND initrd=/tce/boot/core.gz quiet vga=791 norestore swap waitusb=5:UUID="long number" tce=UUID="long number" opt=UUID="long number" home=UUID="long number"
however this is from the extlinux.conf file, I think grub is a little different
In your case, should be tce=hdX,Y opt=hdXY, home=hdXY (wherever you have your TCL). And of course, you don't need the waitusb=5:UUID="long number" as you are not booting from a pendrive
And you'll need to remove all references to home and opt in your filetool.lst file. There is no point in backing up directories that are persistent.
4) No idea, sorry
Hope it helps