You've got a lovely pony and good equipment but we do need to rebalance this whole setup.
Your breastcollar is set a tad high and appears to be cutting into his windpipe when he puts his head down to pull. Dropping it at least a notch should also allow it to lay flatter across his chest instead of tipping upwards so the weight will be distributed more broadly instead of only along the top edge. I really don't like using any sort of shaped collar without a false martingale as they have a tendency to tip up like that and cause more problems than they solve for many horses. A false martingale holds the bottom edge down so the collar lays flat no matter the horse's conformation or the angle of draft.
As you noted, you'll need to get shorter traces or cut the end off the ones you have as that excess strap is likely to trap your reins and cause a real safety concern. You should lower the neck terrets to the current line of the reins and then use them as they will help keep the reins from getting caught.
The main point of imbalance here is your tugs. I see that you got your sliding backband (yay!) but we need to raise both shaft loops quite a bit and it looks like you've only got one more hole on each side; I'm not sure that will be enough. Normal straight shafts would be sitting at the right height so they did send you the correct size/length of equipment, but unfortunately with the marathon shafts the tugs need to be up a bit higher so the shaft itself is level and balanced behind the loop. Yours is going slightly downhill even when you are in the cart. There are a few things we can do to try and fix this, first and most obvious being to raise the tugs as far as they'll currently go. Putting a pad under the saddle will also raise them a little further and might be enough.
The main thing to remember in this case is that your cart itself is adjustable. Can you lower the overall height of the cart and/or raise the height of the shafts a little? The body of the cart is at a decent height for Jack but the way the shafts are so low for both horse and cart makes it look like he's too big for it and creates difficulties with the breeching and the line of draft. The lower the cart is, the lower the center of gravity will be and the more stable it will be. Lowering it will also help the shafts to be more level without raising the tugs themselves further. We still need to raise them so the marathon loops are in the right place but it will help to attack this from both ends!
The other thing is that if the cart is sitting lower, the shafts will be more inclined to float up into their proper position without having to be held there by the tugs. Right now they are going to have a hard time doing that unless you lean waaaaay back. So lower the cart, elevate the shafts
on the cart about half as much as you lowered it, raise the tugs and try putting a thin pad under the saddle so it sits up above his back a little more. They'll still probably look a little low when you first hitch him but when you get in the shafts should float up into their proper position.
NOW...once you've done that, everything else will need tweaking again.
I'd say go ahead and drop the breeching a notch as it's a bit high but I'll wait to comment on how the traces should be run (i.e. through the holdbacks, etc.) until we see how these current fixes effect things. On the plus side your bridle looks well-fitted, your wraps are all done correctly and your saddle is in a pretty good position so yay for that. Can't wait to see the next round of photos!
Leia