Jetta tdi 2000 very rough running

I have a Jetta 2000 TDI, 287,000 miles I was getting a misfire code via VAG-COM on cylinder #2.The engine was running very rough I pulled the valve cover off and checked the clearance from the cam lobs and lifters (lobs in the up position). I found the clearance between the lob and the lifter for the exhaust valve for cylinder #2 in excess of 1/16 of an inch should be ~8K of an inch. So I pulled the head and had a valve job done, a lot of carbon was found in each intake. Cylinder #2 had diesel fuel in it. The cylinder walls looked good and the pistons when brought to TDC looked good. I cleaned the injector outside tip by using a cloth attachment in my bench grinder, was this good for my injectors?
I put it all back together and I still was getting a solid misfire code on cylinder #2, the timing looked good. I pulled the glow plug for cylinder #2 and it was wet. I then swapped the injector cylinder #2 with cylinder #4 and started the car, I am getting the same rough running condition but now no misfire codes. I checked the glow plug in cylinder #2 and it was dry, cylinder #4 was partially wet. So do you think this could be an injector problem? And did I damage my injectors on the way I cleaned them?
Note: New turbo put in 5K miles ago, intake manifold cleaned, used new stretch bolts for head, new head gasket. Injector pump never changed but has always worked. Also have used veg oil in this car from 100K miles to present, have grease car kit installed, I think this is why my injector pump has never gone out.

Get the injectors rebuilt with new nozzles. If they are original then they owe you nothing. VEG oil usually gums up the nozzles in short order...

Touching the exterior of a nozzle with ANYTHING is a VERY bad idea -- I suspect you've destroyed the spray pattern on that injector. Best guess is your injectors are hosed, next-best is that you have IP issues, perhaps (you hope!) in the fuel delivery valves. I would send those injectors off to be tested and rebuilt as required.

I don't see a compression check in the list of things you looked at. That you had the head off should have (did?) gotten a decent look at bore and piston crown condition but nonetheless it's better to know than guess.

Grease operation on these cars is not a great idea. The IP has electro-mechanical components in it (e.g. the temperature compensator, etc) and they are often damaged or destroyed by grease use. Many good pump shops will not even attempt to rebuild a pump that has evidence of this damage in it when they open them up because they get too many of them back on warranty claims; it's extremely difficult to get all the residue out and if you don't, and some of it breaks free, it'll clog things up again.