Here are my current guesses about the role of various connector lines inside the MultiMode II

DB-25 line descriptions

DB-25 line Role To
1 Stepper A Main 3
2 Stepper B Main 20
3 +5 Volts Main 7 (also 1,2,18,19 through 20 Ohms)
4 Auxiliary D (role?) Jumper 2
5 HV to piezo (-Y) Piezo 5
6 NCAFMJM pin 2 (role?) Main 8
7 HV to piezo (-X) Piezo 9
8 Piezo/head chassis ground Peizo 1; Head 13; Jumper 8
9 -15 Volts Main 26
10 Analog 2 (gain select) Main 17, Jumper 6
11 Vertical cantilever deflection Main 15
12 Green loop (photodiode ground?) Main 27
13 BB2107 pin 5 (2+) though R (role?) Main 9
14 Manual switch mode AFM/LFM (+5 Volts?) Switch 10
15 Stepper C Main 4
16 Stepper D Main 21
17 Head Gnd? Head 1
18 HV to piezo (+Y) Piezo 4
19 Main board ground Main 5
20 HV to piezo (+X) Piezo 8
21 Horizontal deflection Main 33
22 HV to piezo (+Z) Piezo 6
23 NCAFMJM pin 3 (role?) Main 25
24 +15 Volts Main 10
25 AD620 pin 2 (in -) through R (role?) Main 31

Main board line descriptions

Main line Role To
1 Stepper C, from DS3658N pin 6 Stepper Black
2 Stepper A, from DS3658N pin 1 Stepper Brown
3 Stepper A? in DB-25 1
4 Stepper B? in DB-25 15
5 Main board ground (black loop) DB-25 19
6 Manual stepper switch direction Switch Purple
7 +5 Volts DB-25 3
8 NCAFMJM pin 2 DB-25 6
9 through R to BBOPA2107 pin 5 (+2) DB-25 13
10 +15 Volts DB-25 24, Head 5 though 10 Ohms
11 Photodiode D Head 11
12 Photodiode A Head 9
13 DG403 pin 10  
14 internal plane, but not ground loop?  
15 Vertical cantilever deflection 620 pin 6 (out) DB-25 11
16 DG403DJ pin 6 DB-25 11
17 Gain select DG 419pin 6 (through R) DB-25 10
18 Stepper D, from DS3658N pin 8 Stepper Orange
19 Stepper B, from DS3658N pin 3 Stepper Yellow
20 Stepper C? in DB-25 2
21 Stepper D? in DB-25 16
22 AD827(far) pin 7 (out) (Tapping-piezo voltage) Head 15, tipholder 6
23 Green loop Head 14
24 Manual stepper switch enable Switch grey
25 NCAFMJM pin 3 DB-25 23
26 -15 Volts DB-25 9, Head 7 through 10 Ohms
27 Green loop DB-25 12
28 Photodiode ground (green loop) Head 2
29 Photodiode C Head 10
30 Photodiode B Head 8
31 AD620 pin 2 (in -) through R DB-25 25
32 BBOPA2107 pin 1(out1) through R(total photodiode)  
33 DG403 pins 1 and 3 (drains from 1)(Horizontal deflection) DB-25 21
34    

Chip list

(following this numbering)

Index Chip Description Role
1 DS3658N Current sink. Stepper motor current sink
2 H7555IBA CMOS timer. Manual stepper motor control clock
3 "NCAFMJM" ? Stepper motor
4 AD827JN Dual op amp. Far side amplifies tapping piezo signal (out Main 22)
5 Scratched out ? Stepper motor?
6 Scratched out ? Stepper motor?
7 AD534KD Difference multiplier (X1-X2)(Y1-Y2)/(10V)+Z2. Photo-diode?
8 AD734BQ Identical to AD534, but with control over denominator. Photo-diode?
9 SG531P 25.0000 M 25 MHz crystal oscillator. Photo-diode?
10 BBOPA 2107AU Dual op amp. Photo-diode?
11 DG419DJ CMOS analog switch. Photo-diode?
12 DG403DJ CMOS analog switch. Photo-diode?
13 AD534JD Identical to AD534KD, but with slightly more error. Photo-diode?
14 AD637JD RMS-to-DC converter. Photo-diode?
15 AD620AR Instrument amplifier. Photo-diode?
16 BBOPA 2604AU Op amp. Photo-diode?
17 DG411DJ Quad CMOS analog switch ?

Main board wiring

Vertical deflection (Main line 15) comes from pins 6 and 8 (shorted together) of the DG403 switch. Pin 6 drains pin 5 and pin 8 drains pin 9 when the switch is turned on. I'm not sure what pin 5 is attached to. Pin 9 is connected (through a resistor) to the output (pin 12) of AD534a.

Manual switch connector line descriptions

See my switch notes for details on understanding the stepper control switch.

Line Color Role To
1 Orange Laser LED ?  
2 White-red STM mode LED DB-25 17
3 Green Mode TM Main 13
4 Blue Mode STM 120 Ohms to DB-25 17
5 Purple Stepper direction Main 6
6 White-brown Stepper switch +5 Volts Main 7
7 White Laser LED? DB-25 17
8 Yellow Laser LED?  
9 White-brown STM mode LED 160 ohms to DB-25 17??
10 Red Mode AFM/LFM, +5 Volts DB-25 14
11 Grey Stepper enable Main 24
12 Black Stepper switch Gnd Main 5

AFM head micro-D 15 connector line descriptions

outside female from top-left: 8 7 6 5 4 3 2 1/15 14 13 12 11 10 9

inside male (on board) from bottom-right: 8 7 ... 1/9 10 11 ... 15 blank

Line Role To
1 Laser Ground DB-25 17
2 Photodiode ground Main 28
3 +5 Volts Laser Power no main, no DB-25 ??
4    
5 +15 Volts DB-25 24 through 10 Ohms
6 STM current? Jumper 1, tipholder 2
7 -15 Volts DB-25 9 through 10 Ohms
8 Photodiode B Main 30
9 Photodiode A Main 12
10 Photodiode C Main 29
11 Photodiode D Main 11
12 AFM tip Jumper 3, tipholder 4
13 Chassis ground DB-25 8, Jumper 8
14 Tapping-piezo ground (main board shorts to photodiode ground) Main 23, tipholder 5
15 Tapping-piezo voltage Main 22, tipholder 6

(see, e.g. Glenair for Micro-D-Subminiature connector descriptions.)

AFM head to tipholder line descriptions

Labeled looking down on tipholder along laser, with MultiMode LCD at bottom from top-left: 1 2 3/4 5 6

Line Role To
1 +12 Volts ?
2 STM current? AFM connector 4
3 -12 Volts ?
4 AFM tip? AFM connector 12
5 Ground AFM connector 14, main 23, main board shorts to photodiode ground
6 Tapping-piezo voltage AFM connector 15, main 22

On our tapping-in-air tipholders, removing the connector-pad plate shows lines 1-4 are not connected to anything. Lines 5 and 6 have wires heading over towards the piezo, as you would expect. On our tapping-in-fluid tipholders, the pad is not removable, but the only wires leaving the pad area connect to the oscillating piezo region, so both tipholders have identical interfaces to the head, with 5/6 providing piezo oscillation and 1-4 as non-contacts.

Since both tapping mode pins are shorted through the head to the main board, but not to the DB-25 connector to the NanoScope, we assume the tapping oscillation is being generated on the MulitMode main board itself.

Piezo connector line descriptions

outside male from top-left: 1 2 3 4 5/6 7 8 9

inside male (on board) from top-left: same + blank

DB-25 labeled HV: 5,7,18,20,22

Line Role To
1 Ground DB-25 8, Jumper 8
2   no db
3   no db
4 +Y piezo DB-25 18
5 -Y piezo DB-25 5
6 +Z piezo DB-25 22
7 Piezo cap Jumper 7
8 +X piezo DB-25 20
9 -X piezo DB-25 7

Jumper pin descriptions

inside male from top-left: 1 2 3 4 5 6 7 8

Roles from MultiMode manual, 14-9

Pin Role To
1 STM current Head 6
2 Auxiliary D DB-25 4
3 AFM tip Head 12
4 Analog 2 DB-25 10
5 Gain Select Main 17
6 Analog 2 DB-25 10
7 Piezo Cap Piezo 7
8 Ground DB-25 8, Piezo 1, Head 13

LCD connector descriptions

inside male from top-left: 1 2 3 4 5 / 6 7 8 9 10

Pin Role To
1 Manual switch AFM/LFM, +5 V DB-25 14
2 Total photodiode voltage Main 32
3 -15 Volts Main 26
4 +15 Volts Main 10
5 Manual switch STM mode Switch 9
6 Head Gnd? DB-25 17
7   Main 16
8 Green loop Main 27, DB-25 12
9   Main 13
10 Horizontal deflection Main 33

LCD board

inside male from top-left: 1 2 3 4 5 / 6 7 8 9 10

Pin Role To
1 +5 V Big regulator
2 Total photodiode voltage  
3 -15 Volts  
4 +15 Volts  
5 Manual switch STM mode  
6 Head Gnd?  
7   Main 16
8 Ground Black loop
9    
10 Horizontal deflection top center BBOPA though R