Chirp on CW receive
Also noticeable on SSB with extended low-frequency audio content!
Sometimes triggered by noise pulses.
The problem was caused by a dirty ceramic trimmer capacitor, TC3001 on the AF Unit. It controls the BFO PLL frequency range.
The obvious cure would be to replace it but spinning it back and forth a dozen times seems to have cured it.
This problem requires further investigation as to why sudden changes in audio content can effect the BFO frequency. Probably a faulty supply decoupling capacitor but since almost every stage of the AF board has it's own decoupling, finding it could be very difficult.
Instability on AM receive
Since I obtained the FT1000 there has been a minor problem with AM receive in the form of instability/self oscillation if you tuned off the centre frequency. This slowly became worse, to the point where any attempt at listening to an AM transmission resulted in random variable frequency oscillation, at all times.
Examining the AF unit with the DVM and oscilloscope revealed nothing and I gave up, several times.
Eventually I decided to turn off the computers and concentrate on this particular problem.
I noticed that any physical movement in the lower right hand corner of the IF board, resulted in the pitch of the oscillation changing. So I lifted the board and looked for dry joints. Nothing.
I removed all of the multi-pin connectors and cleaned them. No change. Whilst replacing one of the connectors, with the rig running, the problem disappeared. Close examination around the connector revealed nothing. So I removed/replaced the plug a few times and noticed that my thumb was pressing against an electrolytic adjacent to the connector every time I pulled the connector out. Pulling/pushing the capacitor turned the fault on/off. It was all down to a leaky 1uF. The capacitor is the output feed to the the AF unit and any DC leaking through upsets the following unity gain voltage follower stage. It also upset the VOX on ssb that had been intermittent for some time. The vox was fine on CW so I never got too concerned about that problem.
A new 1uFd 50v C2126 cured the problem completely.
Display Unit problem
Switching the rig on one day, the tens of MHz digit on the B vfo showed  when it should have shown nothing because the B vfo was on 1.828MHz CW. I wasn't too concerned because swapping A/B vfo's showed the correct frequency on the main display and I don't use the B vfo that much. However, whilst the rig was in bits, during the AM fault finding, I decided to see if I could find the problem.
The first thing I found on the display unit was that the 48volt dc display supply was still 48volts even with the rig power off. The problem is that powering down the rig disables the cpu on the display board which then leaves zero load on the 48volt supply, so it stays there, for hours.
You need to be very careful if you decide to carry out any work on the display unit, otherwise it could be catastrophic. I have fitted a 56k resistor across the 48v so that when I switch off, the supply falls to less than 3volts within a few seconds, so you won't blow all the decoder chips if you slip with the meter prod.
The decoder chips, unfortunately, are mounted behind the display and since the display is made of glass and has a lot of pins fixing it to the pcb, you need to be very brave, or foolish, if you decide to replace a driver chip. I simply chopped off all of the pins from the chip from above, then removed the left over pins with the soldering iron and solder sucker. I then fitted a turned pin dil socket to the board so that I could afford to apply heat from above without the risk of blowing another chip. Not too much though or you will melt the socket. Since I use HamRadioDeluxe quite regularly I could still read frequencies etc. even with the rig display non-functional.
Of course you could simply buy a new display board (no longer available from the manufacturers) but I strongly object to paying out 150 quid because a 75p chip has fallen over.