If you check the update to the previous log entry, the board temps were getting up to 290 degrees Celsius. So after thinking about it for a bit, the thermocouples floating inside the oven are basically next to useless for any sort of temperature regulation as they don't correlate to any meaningful and reproducible temps, no matter the board colour.

Now it's time to replace the thermocouples. The main issue is how to route the thermocouples. Firstly the existing thermocouples are glued into the chassis, so removal is difficult. And secondly, where they come out is a bit tricky from a cable management point of view, since the tray slides in and out (i.e. how are you going to deal with the excess lead and how do you stop it from knocking parts off when you slide it back in).

So to deal with this a new route was found. This was actually easy to do without any mods as the forced air extraction system already has a way to go without modifying the case (there's a small hole for entering this section which the power lead for the secondary fan goes through):

Inside the flue section on the left of the image above, there is some vent holes that go into the case, so you can just feed the thermocouple through those vent holes and you're in. Be careful when putting the case on now so the thermocouple wire doesn't get crushed.

Now inside the case, you can feed the thermocouple on the right side of the tray in the grove and you can tie off the excess with some steel wire such that it moves under the tray when you slide in and out in a concertina fold, leaving just the end piece to worry about when positioning it (i.e. just tape it to the board and you're done).

With all that done, you can now get an almost perfect thermal profile and it's guaranteed to correspond to the actual board temps. Note I was using two board colours in this test and the graph is drawn based on the average of the two temps.

We're ready for prime time!