Multiple Problems

I am having at least two problems right now.
1. The firmware is timing out before the right extruder reaches the designated temperature (it gets to about 180 and then stalls). Print temp is set for 220 (probably a little high for PLA but I am experimenting with different temps to see what the effect is).
2. The quality of prints is very poor. I was getting much better prints a while ago with essentially the same print settings and the same print files. One thing that may be an issue is that I have had to clear jammed filament (I have only used PLA) by disassembling the extruded and using drill bits to clear the filament after removing the nozzle. In the process I poked a hole in the PTFE tube that goes in the extruder and had to replace it. I was unable to find an exact fit but I bought some 3mm OD, 2mm ID PTFE on ebay which turned out to be slightly larger OD than the original tube. I was able to get it installed with some difficulty however and have made multiple prints since then of mostly poor quality. I have installed a glass plate on the print bed and, with hair spray, am able to print without rafts but am experiencing very poor quality, especially on the first few layers. I also note, that before I installed the glass plate, the prints with rafts were impossible to separate from the rafts after printing, which wasn't the case in the past.

Could it be that I need new extruders and/or nozzles? I would be willing to pop for new extruders if I knew that they were higher quality and would solve my problems but I don't know if that would be the case and I don't know what extruders to buy. I did buy some new nozzles but they have a smaller ID than the ones I had and the PTFE tube will not fit into them.

Any ideas?

sounds like you damaged the nozzle with the drill.
I'd start with new nozzles. The ptfe tube should be fine.

That would be my guess also. I do not use drill bits, my preferred way is to remove the extruder, keep the fan still attached and pre-heat. Then I use a Jumbo paper clip to push down into the heated block and that clears it. Then I also have a 0.38mm guitar string that I can run up and down through the heated nozzle. Let it all cool back down and put it back together. I use a small hex nut to keep the fan on while the extruder is not there.

It is possible that the nozzle is just worn out but I didn't ever use a drill bit to clear the nozzle. My technique was to remove the nozzle, heat the block, then use a 1/16 drill bit gently in the teflon tube. I did that several times and it worked well but one time I got a little too enthusiastic and pushed the drill bit through the side of the teflon tube. I then ordered some 3 mm OD, 2mm ID PTFE tubing on Ebay. It turned out to be slightly more than 3 mm in OD but I managed to get it in the block and get the nozzle back on. Just today I removed the nozzle to inspect and found that the PTFE tubing is burned and broken. That may be the cause of my problems. I don't know why it burned unless it was not PTFE or that PTFE is not the right material. Now I am kind of stuck. I think I can clean out the block but I don't have a tube to replace the original and apparently don't know where to find one. I have tried to contact CTC to see if I can buy any parts from them but they haven't replied.