OK lots to unpack here. Go grab a coffee, lol
1. I'm not 100% sure on this one, but I'm thinking that these terminals will have more than wire attached to them in the schematic. However, I can't be sure. Check your schematics and make sure that you're not double-landing any wires on them. If that's not the problem, can you post one of the drawings that has a problem terminal in it?
2. Two ways to handle this one. First, just put in a note that says something along the lines of 'THOU SHALT JUMPER ALL OF THESE THINGIES". Second, you could just draw a graphical jumper over top of the terminal strip after it's generated. BUT!!!! Please see the note below about your terminals, and your wish to jumper everything in that one strip.
3a. (I'm splitting #3 into two answers.) You can insert multiple footprints at once, if you are inserting them from the schematic list. (This is the only workflow that I use for drawing panel builds, so my advice is pretty one-sided here.) To do this, Go to Panel>Insert Component Footprints>Schematic List. This command pulls up all of the components and devices in your schematics, gives you a list, and then allows you to place the footprints. When you select multiple components, you're given the option of selecting where each one goes, or to input a certain set distance. That second option will put them all in a straight line, left to right, at whatever distance you tell it. (I'm willing to bet that if you put in a negative value here, it will lay them out right to left, but I've never actually tried it.) I keep a list of 'footprint spacings' just for this purpose. If I'm about to put in a bunch of circuit breakers, for instance, I'll pull up my little document, see what the spacing is for that component, and then type it into the box. I've laid out 48 inches worth of circuit breakers at once like this. But I'm not sure if there is any other workflow that will do the same thing.
3b. And as for footprints that aren't just plain rectangles...well, you can draw whatever you want, and then there is a tool that will add that to the Footprint Lookup Database. The basic workflow is this: *Draw the new footprint; *save it as a dwg in your AeData folder; *use the editor to assign your new footprint's dwg to the part number; *insert the new footprint. There's more to know, I added a little bit of that below. The editor tool is found at Panel>Other Tools>Footprint Database Editor.
Now for extra info and notes:
First, on jumpering that entire terminal strip: Jumpering forces all the terminals to carry the same electrical signal. But in that strip, you appear to have a different signal (or, if you prefer, wire number) on each terminal. Without knowing more about your schematics, it's impossible to say. But from where I sit, there is something here that isn't right. Usually if you're jumpering terminals they have the same wire number.
Next, your terminal footprints: The ones in your drawing are the 'default' terminal footprint. It probably is NOT the same size as Automation Direct terminals that you're using. (Actually, you only have the part number assigned to a few of the terminals. But whatever part numbers they are, the default terminal footprint isn't likely to be the same size.) Size is especially important for terminal blocks. You could find that the vertical space you reserved for terminal strips isn't enough because in real life they happen to be 0.375" wide instead of the 0.250" that they are drawn at.
You should consider creating a footprint for each part number you use, unless one already exists. These will have to be added to the Footprint Database using the editor. This goes for every component, not just terminal blocks.
Footprints in general: Having good footprints is, IMHO, one of the most important and one of the most overlooked aspects of using ACADE. I'm constantly surprised at how many people are satisfied with empty little rectangles. We make our panel drawings as realistic as they can be. I download models or other CAD files from the manufacturers and base my footprints on them. Sometimes I have to draw them based on a dimension drawing I found in a PDF. Regardless, at this point, I use exactly zero of the out-of-the-box footprints. They all suck, and most of them don't have wipeouts. To me, every footprint should have a wipeout to hide the DIN rail, and they should all look more or less like the component they represent.
I'd recommend these guidelines when creating footprints:
*consider your plot size. If you have to frequently represent a 72" tall control panel on an 11x17 sheet, like I do, then you're not getting much fine detail into your footprints. Remove unnecessary linework to prevent blurry crap from ending up in your layout print.
*always make your base point in the footprint 0,0,0.
*always run PURGE after you draw the footprint to remove any unnecessary objects.
*for ACADE footprints, I would put everything in the footprint onto Layer 0.
I attached dwg's of two of my panel layouts, without title blocks. Feel free to use anything in there in your own stuff.
Hope this helps,
Jim

Jim Seefeldt
Electrical Engineering Technician