In the panel cfg, comment out the entries below in red. That should fix the autopilot.
Moses
[Window00]
file=Ju88C.BMP
file_1024=Ju88C.BMP
size_mm=800
window_size_ratio=1.000
position=0
visible=1
ident=MAIN_PANEL
render_3d_window=1
window_size= 1.000, 1.000
window_pos= 0.000, 0.000
gauge00=MAPE_Luft_4Eng2!ManifoldPressure2, 749,435,52,51
gauge01=MAPE_Luft_4Eng2!Tachometer1, 695,465,52,51
gauge02=MAPE_Luft_4Eng2!Tachometer2, 749,493,52,51
gauge03=bf109e!Attitude, 435,389,77,76
gauge04=extra-300!Master-Switch, 261,476,12,12
gauge05=extra-300!Avionics Switch, 275,476,12,12
gauge06=MAPE_Luft_4Eng2!ManifoldPressure1, 694,405,52,51
//gauge07=Ju88!Repeater Compass, 520,375,72,88
//gauge08=ASKANIA.remote_compass_rp, 364,387,63,24
gauge09=fw190a!Airspeed, 235,500,60,65
gauge10=fw190a!Altimeter, 288,423,64,72
gauge11=fw190a!Vertical_Speed, 302,502,59,59
gauge12=fw190a!Fuel_Warning, 708,535,10,10
gauge13=bf109e!Turn_Indicator, 360,420,66,66
gauge14=f6f3_hellcat!Hydraulics, 469, 366 ,9,9
gauge15=bf109e!Gear, 735,551,50,50
gauge16=f4f4_wildcat!Icon-Engine-Controls, 542,358,13,13
gauge17=f4f4_wildcat!Icon-Map, 714,386,13,13
gauge18=concorde!Avionics-Display-Toggle, 555,358,13,13
gauge19=concorde!Fuel-Panel-Display-Toggle, 568,358,13,13
gauge20=bf109e!Flaps, 216,535,18,65
gauge21=mooney_bravo!Autopilot Switch, 528,358,12,12
gauge22=concorde!Compass-Display-Toggle, 701,386,13,13
gauge23=Ju88_Klappen, 677,555,43,42
gauge24=fw190a!Heading_Indicator, 602,382,80,81
gauge25=bf109e!Heading_Indicator, 261,563,61
[Vcockpit02]
Background_color=0,0,0
size_mm=512
visible=0
pixel_size=1024,1024
texture=$_panel_1a
gauge00=fw190a!Clock, 128,390,120,111
gauge01=bf109e!Turn_Indicator, 258,256,127,124
gauge02=MAPE_GerTwinMags!Magneto 2, 372,-1,43,175
gauge03=MAPE_GerTwinMags!Starter2, 286,57,67,65
gauge04=MAPE_Luft_4Eng2!Oil Temperature 2, 257,129,125,125
gauge05=MAPE_Luft_4Eng2!Fuel/Oil Pressure 2, 388,259,125,125
gauge06=MAPE_Luft_4Eng2!Radiator Temp 2, 130,130,125,125
gauge07=MAPE_Luft_4Eng2!Tachometer2, 129,257,126,126
gauge08=MAPE_Luft_4Eng2!ManifoldPressure2, 387,129,125,125
gauge09=MAPE_Luft_4Eng2!Oil Temperature 2, 2,129,125,125
gauge10=Ju88!Course Deviation Indicator, -2,300,131,54
gauge11=Ju88!Course Selector, 247,379,134,133
//gauge12=Ju88!Repeater Compass, -2,363,130,147
gauge13=ju88_gyro, 379,384,135,131
Also, the CFO_REFUEL_DUMP gauge does not work in FS2004 (never has for me anyways). You should comment that one out as well.
[Window03]
file=AuxPanel_AP.bmp
file_1024=AuxPanel_AP.bmp
size_mm=236,184
window_size_ratio=1.000
position=0
visible=0
ident=RADIO_STACK_PANEL
sizeable=1
render_3d_window=0
window_size= 0.230, 0.240
window_pos= 0.770, 0.760
gauge00=concorde!Roll-Trim, 169,112,57,56
gauge01=Cessna!Rudder_Trim, 165,71,62,39
gauge02=concorde!Clock, 106,60,54,54
gauge03=prop2ERKadf, 7,60,96
gauge04=prop2ERKap, 7,3,222,55
gauge05=GA_KneeBoard, 214,62,15,14
gauge06=Cessna!Pitch_Trim, 107,117,33,60
gauge07=concorde!Fuel-Panel-Display-Toggle, 164,62,13,13
//gauge08=CFO_REFUEL_DUMP, 8,116,93,63