Just stumbled across this.. I train racing Standies (pacers) and thought I'd clear a few things up.
Firstly, I seriously doubt your horse is a Sec D. I've never heard of anybody trying to race one and I don't know why anybody would try since a Standardbred would beat a Sec D every time. Are you sure the previous owner didn't tell you he was a Sec D to try and sell him for more money? This happens a lot as Standies are not popular riding horses (I have NO idea why as I would never want to ride anything else), although usually the unwitting buyer will be told it is a TB or TBx.
As for the rubs you describe, it sounds to me like terrible abuse of the hopples. They are NOT meant to cause this sort of damage, and they are not supposed to be used to make a non-pacing horse pace. Some breeds (like Standardbreds, Icelandics and many others) pace naturally and all they need is a little encouragement to pace at high speed. Hopples are made of soft, flexible, lightweight plastic and are there to encourage them to pace without breaking into a gallop. If the horse starts to 'skip' his leg will hit the hopple and that will remind him to shorten his stride and stay in a pace.
If the hopples are adjusted correctly they will not cause any damage or pain whatsoever. If the hopple is set up incorrectly or the horse is sore, for example, he might rub then. But not if everything is right. We bought a horse 6 weeks ago who had had a terrible time for various reasons, one of them being her harness which was set up all wrong. As a result she had bad hopple rubs and the skin was raw in patches. After a few small changes to the tack we tried her a few days later and the hopples didn't even knock the scab off. Then it was just a case of getting her happy and showing her that her harness is not going to hurt her, and I'm pleased to say she won 5 weeks later at 10-1 (her first win in 13 months).
Pacing comes very naturally to a pacing-bred Standie. Of the 3 I have, the mare I just described paces all the time when you ride her without hopples (which is how I do 90% of the training). My oldest horse who is 16 will walk, trot, pace, canter, gallop or do a running walk on command - he also jumps like a stag. The third horse very rarely paces unless he's excited. When their blood is up most pacers will choose to pace as it comes naturally to them.
Could you post a photo of your horse and the rubs?
I hope this has been of some help :)