It sounds like your phono cart has enough time on it so its fully broken in. Just be aware that when it comes to break in, nothing is like a phono cart. The difference is huge. I've had brand new units that I thought were defective because they sounded so bad right out of the box. For the first 20 hours, or so, I can hear a difference from record to record. As for cables, they break in too, and one of the difficult things about vinyl is to break in a tonearm cable, it has to be done manually with records. Its not like a CD that you can leave on for a couple of days. For me, I like Audioquest cables with the DBS system. The DBS system was designed to make break in faster, and stay broken in for longer times. While possible, I don't think this is your problem either. However, if you try a bunch of things that don't work, maybe have a look at the cable.
I would start off with 2 things. The first is to make sure the problem is TT related, and not something else in the system. Does the issue only occur when you play vinyl, or will a CD player or streamer show the same problem, as well? If so, the problem lies elsewhere. If it is isolated to the TT, I would go over all of your alignment angles. You may be right at a threshold, and putting all of your angles back into spec may fix the problem. If everything is in spec, look at the values for each angle and maybe try some small adjustments while still keeping everything within range.
If you want a really good setup guide, Brooks Berdan did a complete setup process that was published in The Audio Perfectionist Journal. If you do a search, you should have no problem finding it. If not, go to Vandersteens website. You'll find every APJ issue to download for free. Its a really good guide. I thought his comments on VTA/SRA were particularly helpful.