For detailed Boeing 727 systems/checklists etc, please view our system technical link page here. I don't have a copy of the FlyJSim 727, but having a few thousand hours on the real thing, I'll try to give a tutorial from the top of my head. The tutorial is based upon a Boeing 727-200ADV with JT8D-15A's, no Nose Gear Brakes:
Aircraft Limitations:
MTOW: 86,409 Kgs
MZFW: 63,503 Kgs
MLAW: 73,029 Kgs
Max T/O EGT: 620ºC (max 5 minutes)
Max Start EGT: 575ºC
Maximum Continuous EGT: 580ºC
We'll plan the flight from Cape Town (FACT) to Johannesburg (FAJS) in a 727-200, it doesn't matter whether it is a freighter or pax model. The fuel required for the flight is 18,000 Kilograms with a burn of 9100 Kilograms, we will take Durban King Shaka (FALE) as an alternate. The Maximum Take Off Weight (MTOW) for our flight is 82,129 Kilograms (Landing Weight Limited). For flight planning purposes we will assume either runway 01 or 19 with a direct to JSV after Take Off (be careful for the mountains around Cape Town after departure). The flight time will be around 01:50 minutes, based upon zero wind and a cruise of Mach .80.
Pre-Flight:
If the APU isn't running yet, place the battery switch (located on the top left side of the Flight Engineers panel) to on and check that you have 24V DC (minimum is 22V) with the DC meter.

On the Auxiliary Panel (on the right on the Flight Engineers panel) hold the APU start switch momentarily to start (we won't do a fire warning test). Check the volt meters on the auxiliary panel and check for 115V AC and 400Hz. Select volt meters on the Flight Engineers panel to Bus Tie.


Once the APU is running and has stabilised, place the APU Generator Breaker to "Close" (make sure that the Field Relay light is out, if not close the Field Relay first). Now on the Flight Engineers panel, place the Essential Power selector to APU.

Set the pressurisation panel (dial in Flight Altitude/Cabin Altitude according to flight level (for our flight we will fly at FL330) and Landing Altitude according to landing field elevation minus 200 feet (5360' for FAJS), leave the Flight/Ground Switch in Ground, (assuming it's an electro/pneumatic system) for the "CAB ALT" use the placard to the left of the controller (4800' for FL330). The selector is to be placed and left in the "AUTO" position.

Switch both System B Pumps to "On" and leave the System A Pumps on (we will assume for the pushback that there is a bypass steering pin) and make sure the "Ground Interconnect" is closed.

Let's load the fuel with tank 1 & 3 containing 5500 Kilograms each and the number 2 tank with 7000 Kilograms (there's an extra 1000 kilograms in the number 2 tank for the APU fuel burn). Load your aircraft as you desire, but do not overload the airplane.

Cape Town weather is assumed to be 15ºC with a QNH of 1013. We will do a Flap 15 Take Off today. Our V-Speeds and EPR's should be set to:
EPR1: 2.10 EPR2: 2.12 EPR3: 2.10
V1: 142 (white plastic bug 1)
Vr: 143 (white plastic bug 2)
V2: 154 (orange command bug)
V2+10: 164 (white plastic bug 3)
F5: 180 (white plastic bug 4)
F2: 210 (white plastic bug 5)
F0: 220 (white plastic bug 6)
For this tutorial purpose, I will only explain how to "align" the INS, I won't go into detail on how to load the waypoints into the INS. Place the INS Mode Selector to "STBY"

On the INS, place the selector knob to "POS" and insert you're current latitude (press the number 8 which will give you South), once the latitude is correctly displayed, press "INSERT". Do the same for the longitude (press 6 for East).
When done with inserting the coordinates, place the INS Mode Selector switch to "ALIGN"

You can see the progress of the INS by placing the INS selector knob to DSRTK/STS. Let the INS countdown all the way to 05.
Before Start:
Now that we're done fuelling, let's switch on the fasten seatbelt sign, check that the emergency exit lights are armed and set the parking brake.



Set your radios for the departure (Cape Town VOR, CTV:115.70) and set your transponder to 2000.
On the right side of the overhead panel switch all "Window Heat" switches to "on".

Once the INS has counted down to 05, place the INS Mode Selector to NAV. Do not taxi out without the INS Mode Selector in the NAV position, this will render the INS useless for navigation and it can be used for Attitude Reference only.

Read the "Before Start Checklist".
Cleared to start:
On the Flight Engineers Panel, set all Engine Bleed Switches to open and switch off both Pack Valves (observe the duct pressure increasing to around 40 PSI, minimum is 30PSI).

The Hydraulic Panel was already set in the Pre-Flight, but normally we would switch on both hydraulic B pumps and switch off the A pumps if we were to push back.
Switch on 1 Fuel Pump in fuel tank 1 & 3 and 2 Pumps in Tank 2 (Left Forward & Right Aft).

On the overhead panel, switch the Anti Collision light on and complete the "Before Start Checklist" below the line (if applicable).

On the overhead panel, select the "start valve arm" to arm and place the Number 1 Start Switch to "Ground"

Observe the drop in duct pressure on the Flight Engineers panel:

After the starter has engaged and the duct pressure has dropped we should see an increase in N2 RPM and on the Flight Engineers panel we should observe a rise in oil pressure:


At 15-18% N2, move the Start Lever to the Start Position, monitor the Fuel Flow (max 500Kg/h) and check that the start temperature (EGT) does not exceed 575ºC. At 35% N2 release the start switch and observe the rise in duct pressure again.

Repeat the same for engines 2 and 3.