Now, I can't stress this enough... it's something so simple but people do not seem to understand.
Before you do any repairs, check for fault codes! Next thing is to pressure test the cooling system and radiator cap when the engine is cold! Doing this procedure will shed a light on any external coolant leaks, eg. radiator and heater hoses, water pump gasket, thermostat gasket, heater valve etc. It can also pinpoint internal coolant leakage, eg cylinder head gasket (bubbles in the radiator filler neck can indicate a blown head gasket).
Your main issue is an overheating problem correct? There are many causes to this issue. I'll start with the simple troubleshooting first.
1. Check your engine oil level. - A low engine oil level can play a huge part in engine overheating problems.
2. Clean your radiator core. - Grab a garden hose and give the radiator a good thorough clean, side to side slowing making your way from top to bottom. Front and back sides too.
3.Check the coolant level. - Now, check the condition of the radiator cap (A pressure test on the radiator cap will maybe show signs of a damaged pressure valve) and check the coolant level at the radiator filler neck. If low, top up with coolant or distilled water until it starts to overflow from the radiator neck and then reinstall the radiator cap. Then fill the coolant reservoir bottle to the full mark also. I'll talk about bleeding the system shortly.
4. Check the cooling system electrical circuit. - Your best friend is a multimeter here.
Fan cut in temperature
Low speed - 104C plus
High speed - 109C plus
Fan cut out temperature
Low speed - minus 100
High speed - minus 105
Cooling Fan Test Procedure.
With the engine cold, turn the ignition on and make the sure the cooling fan isn't rotating. If it doesn't rotate, disconnect the coolant temperature sensor ( The larger sensor under the thermostat housing) and start the engine. After around about 15-20 seconds the cooling fan should start spinning at it's low speed, and after another 5-10 seconds the fan should increase to it's high speed. This check means that the fan circuit works fine. If not, however, you need to check the relays and terminals for continuity as you could possibly have a wiring short or a faulty relay.
5. Check the cooling system components. - First off, the thermostat. Remove the top radiator hose and thermostat housing and then you have access to the thermostat.
Thermostat.
Opening temperature - 90C
Fully open temperature - 106C
Get a saucepan and fill it with water and boil on the stove. Grab the thermostat with a pair of pliers and place it in the saucepan, with the thermostat fully submerged. Then grab a thermometer and place it in the saucepan as well. Keep an eye on the temperature and the thermostat to check for correct operation. If not within spec, bin it.
Now, if you plan to remove the water pump to inspect it, I'd just bloody well buy a new one. $40 for a new water pump and gasket for a VN-VS V6, cheap as chips.
When you have the thermostat and radiator hoses removed, I recommend to flush and reverse flush the engine block and radiator with clean water. What I mean by this is, hose in thermostat cavity water flows out lower timing cover pipe and vice versa. Same for the radiator, hose in inlet side, water flows out outlet side and vice versa. Continue flushing until clean water flows nicely.
Bleeding the cooling system.
Now, with the coolant level correct and the cooling fan circuit operational, start the engine. Grab a flat blade screwdriver and slowly loosen the bleeder screw on top of the thermostat housing until a stream of coolant appears. Open and close the bleeder screw a few times for a minute or two until the cooling fans start rotating. This means the engine has reached operating temperature. Then just open the bleeder screw and continue until a strong, steady stream of coolant is present. Close off the bleeder screw and you're done! Next thing to do is pack up the tools and work area and take it for a test drive!
Also check the coolant level by the coolant reservoir bottle the next day when you wake up and the engine is cold. Top up if necessary.
I hope this helps you out enough.