Half an inch isnt much.
I just had a brilliant idea, if I do say so myself.
Instead of cutting the spring, get some small straps like cheap ratchet straps, feed it through the spring at one (near the) end, feed it down the length of the spring and back out near the other end, lower the deck as far as possible, an inch or more lower than your usual cut height for example. That will compress the spring. Pull the straps as tight as possible and tie ends together. Raise deck to normal height and the springs shouldnt touch the stops. The straps should hold the springs compressed. No need for cutting shorter or messing with deck level etc. Only cost a few $ to try anyway!
Failing that, not sure how but could you add some weight to the deck, a few bricks or something? Just for testing. You could bolt something on later if it helps.
I think the jerking is just something youll have to get used to. Im really doubtful that the drive is faulty. That said, maybe the dampeners are bad. Doubtful both are though.
I really think if you get your body motion sorted, youll sort the jerking.
Put a few more hours on the machine with the backrest angled away and see how you go. Its about all you'll be able to do in the end.