Height of shafts, levelness of shafts on 4-wheeler vehicle is a lot less important than on a 2-wheeler. Still should not be a BIG difference in unlevel, pointing at the sky or dirt. That will change the draft (draught) angle, making vehicle harder to pull, when harness traces are attached too low on the vehicle. Animal gets tired faster hauling his load when he must pull way uphill with his trace line.
Shafts on a 4-wheeler are a control point for the horse, so he can direct the vehicle in turns, hold it for halt or backing. Not a load-bearing point.
Shaft on a 2-wheeler are PART of the whole system of balance and control of the vehicle. Equine carries weight on his back thru the shafts. Having them riding level is REALLY important for his comfort, ride of the passengers, control of the vehicle.
Most 4-wheelers are made to sizes, pony, cob, horse, large horse, that keeps the shafts more horizontal on the equine’s sides. True in the antiques, more common buggies and wagons sold for pleasure riding in newer vehicles. Modern Marathon vehicles are another ball game, rules change there.
You have disadvantages with shafts pointing up or down, catching a rein or bridle on shaft tip is a possible problem when shafts stick up too high. Angle of tips up high can cramp the turning radius of the front end in 4-wheelers with raised shaft heels catching on the front of vehicle because they are not vertical now, but beyond vertical. Heels to curve are now behind the connection points on the front axle, too close to the carriage dash. You can’t make the turn you planned, startles the horse with restriction, so it can be unsafe to drive horse to that vehicle with shafts up so high.
You also do not want shafts down too low on his sides he can hit himself on the sides with his stifle and elbow, get a leg over the shaft or trace.
It sounds like you just need a new pair of shafts that have a higher rise from axle connection to bend at the cross piece behind the animal. Shafts are easily made to fit all sizes of animals, not really expensive to purchase a second pair. Much the easiest and safest way to have things back fitting pony correctly for safe driving.
The harness has been lowered as far as possible, maker does not put longer straps for tug loops because it would be unsafe having lower shafts. So the vehicle shafts need changing to raise their height on his sides. If you are getting them made for pony, get them sized so they ride level, at the height needed on his sides. Witmer’s Coach shop sells and ships shafts all the time. I am sure they or another carriage shop can help you get the correct sized shafts for your pony and wagon.