I'm not sure what you mean by chugging. The best I can describe it is the sound a standard makes when you forget to let off the gas all the way when pushing in the clutch. It just jumps up once, then smoothly goes down to where it belongs at 1700rpm. I maybe wouldn't notice it if my car wasn't so loud lol. It has a custom exhaust that the previous owner put on it. The weird thing is that it only happens when I have it in drive when it hits the shifting speed. If I have it in third until then, it shifts normally as soon as I put it in drive (unless it's cold, then something is delayed, but not sure what).
I'll try the brake tap next time I'm in overdrive. It doesn't happen very often because the top speed limit most places I drive here at school is 40, but I could go down the road where it's 50. If I remember correctly though, I'm pretty sure it does that. It kinda scared me when I noticed cuz I thought something was wrong. Setting the cruise control also does that for me, but I never use it anymore because it caused weird rpm changes when I used it on the highway once.
I'm not really worried about the shifter unless it's contributing to this issue. My dad tried to look at where the cable links up and thought it looked normal, and it hasn't gotten any worse. I may look at it again though.