So most of what you are trying to get around are game mechanics. LOTRO just doesn't do what you can do in WoW and it's rich interface for macros.
On to the answers (kindof).
1. Not likely in a 1 click method. There is not really a method to specifically target a casters pet except cycling. If you press a target party member, and then press it again, it will switch to the pet if the target has one. To make it consistent, you would need to know you were not targeting the party member first, so, this ends up being something like F1, F2, F2, HEAL. So you could potentially do it, and you
might be able to get away with some carefully engineered mapped keys which call other mapped keys, but it will be highly dependant on the game client interpreting the flurry of inbound key presses that it will receive. But that all said. You could try it. I'd start with a mapped key that calls 2 other Do Mapped Key Actions, which are going to do the F1, F2, F2, and put this on a mouseover, and if that works, then all you need is a heal mapped key (which you probably already have).
2. Not on a Clickbar. On a menu, sure. On a Menu it is the Button Margin and Border Size in the menu template. If menus would do mouseovers, then I'd probably redo this guide with menus. I could setup a custom menu template to do that for me, but there ends up being a bit of a disconnect as you then end up configuring things in ISBoxer that don't link anywhere because it is defined in the custom template, and I was trying to keep it simple. All the options under clickbars are a little bit limiting on that front and end up needing individual buttons in clickbars, and then a mapped key to do a lot of loading.
3. Sounds like there may be some trickery going on with VideoFX and transparent buttons. You mention some issue with Targeting and then mix it up with Follow (which yes, the method for LOTRO is select target/follow target), making the question in this item all a bit confusing. Sure you can target a slot. I take you through doing this in the guide. You want to target a specific slot, use the Variable Keystroke Action and choose Target Slot X. You want to Target the active slot, select one of the Target Slot X variable keystrokes, and replace the number with {SLOT}.
If you are having issues with the Quick Setup Wizard Target/Follow method, which should be using the method under ISB-42 Party -> Follow Me (Target Slot), then open a new post in the appropriate forum and
share your config.