Adhesion/Under-extrusion Issue  

Adhesion/Under-extrusion Issue

I am printing a large quanitity of the same part on my MK2 with PETG and have developed an issue which has led to really poor print quality.
I was tweaking the slicer settings each time for the first few prints, but have now stuck with a gcode file for the last handful of prints. Within the parts printed from that same gcode, the issue has occurred. 2 new spools of the same filament (Hatchbox PETG black) were used during this time, the issue not correlating with the change of spool. I first noticed it when I started a print and some of the features of the first layer did not stick. The only features not sticking are the perimeters of the holes. The main perimeters stuck fine, as well as the rest of the first layer. But the hole perimeters seem to just glob up on the nozzle. I played with the live z adjust but considering nothing had changed I didn't change it by too much. I then noticed the issues throughout the entire height of the print, so I assume it's not just a first layer sticking issue. That's what makes me think it's an under-extrusion issue. Nothing seems to be adhering together (layer-to-layer or even lines next to each other in a layer). See the attached picture of the internal standoff which has significantly deteriorated in quality.
As I mentioned I went through a few different gcodes before settling on the one I have now, but the one I use now produced good parts for the first few times. One of the things I changed in those early gcodes though was turning the speeds up. I am wondering if I am seeing wear/damage from running too fast. (I don't remember the exact values, I'll have to post that when I get home)

So last night before I printed again I tried a few things:
First, I hot unloaded the filament to see the extruder gear. There wasn't any powder or anything in there (overall looked clean) but I took an air can and blew out the whole area. Then I used the acupuncture needle to clean the nozzle from the bottom upward. I did this a handful of times and nothing felt clogged.
I then checked the diameter of the filament and made sure it matched slic3r.
I checked my extrusion multiplier by extruding 100mm and about 94mm went through, so I left my existing multiplier of 1.06.
I printed a single layer 1" square with the same exact slic3r settings as my part and it produced a nice, well adhered square.
I manually slid the x and y axis and didn't feel binding, but put some oil on the smooth rods anyways. My y-axis bearings have been noisy for a while.

I printed after those checks and nothing had changed, same issue.

From what I see online, I think the next step is to try a cold pull. (I read for PETG you run it to 230 then to 100 then pull?)
I also read that it's possible I deformed the nozzle with my pliers, since I use them to clear the dripping filament just before each print. I am typically very gentle but I guess this is possible.
I have also not turned off or restarted the printer for a long time (before I started all of these prints). I use octoprint on a raspberry pi and that has not been restarted either. Maybe I should do that tonight too.
I could try a single width cube to check the extrusion width, but since this issue happened with the same gcode and within a spool of filament I don't think it's a slic3r setting issue. This same combo printed well at the beginning. So I assume something is clogged up?
As you can see in the picture of the bottom of the 2 parts laid next to each other, the first layer quality overall doesn't seem to have changed much. It just doesn't do the small perimeters well. And as I mentioned, the issue is throughout the print height.

Any ideas are appreciated. This is the first time I am actually being paid for a print and I'm on a tight timeline so I need to sort this out ASAP.