Well, I may have fixed it boys! Fingers crossed!
Here's what I did:
1. Did all electrical checks: fuse box 2 where the DPS' 40 A fuse is; cluster gauge connector; DPS power connector, ground connector, and control connector all passed the test as per the service manual; battery voltage while OFF, during cranking and while running also checked out;
Nothing wrong here.
2. Removed the DPS' motor cover (stator) and I found that part of the magnet's surface inside the cover is rough and pitted even though there were no signs of water or moisture intrusion or rust. I used a very fine sandpaper to get rid of the roughness and sanded it back to full smoothness and put it back together.
Went for a test drive after that and the symptoms were greatly reduced but still there; 50% I'd say.
3. During the test drive, I noticed that the main (thick) electrical harness that goes from the back to the front on the right side was sitting too close to the engine (front cylinder area above near the front chain tensioner) and hence was very warm. This might have happened while I was adjusting the valves last time. I used a small zip-tie to lift it up and distance it from the engine.
After that, I felt as if the problem was 90% gone.
4. Upon further inspection, I found the three sensors that go into the right side of the gearbox to be a bit loose as they were weeping a bit of gearbox fluid. I tightened them well and then went for a test drive and the problem was completely gone. I tried to load the DPS as much as I could during the ride to try and replicate the problem but I couldn't. Everything felt normal again but I must note that it was getting darker and cooler.
I want to say that it's completely fixed but I won't until I go for a full ride during the day when it's warmer and test it rigorously.
I don't know which of the above contributing factors was/were the cause of the problem but logically it could've been a mix of the magnet's pitting, the warm harness, and the speed sensors looseness resulting in erroneous/garbage signals being sent to the DPS unit and hence causing the stuttering. Garbage in garbage out. You know the drill.
I'll definitely report back once I go for a full ride but looking forward to hear your thoughts in the meanwhile.
Although I hate it when my machine is down, but I must admit that wrenching on it and getting to know it more and more creates this amazing bond with it. I love this sport and I love this community. Thanks to everyone who chimed in.