The small cables you are referring to are, I believe, the ones that are included with most base plate kits. It is a fail safe that is meant to attach the base plates to the frame of the vehicle just in case something happens and the base plates break away from the truck.
You will still need longer safety cables such as # RM-649 that you have referenced to go from the base plates to the RV.
In addition to the tow bar, base plates, and safety cables, you will also need lighting on the truck and supplemental braking if you do not have them already.
For lighting you can use bulb and socket kit # RM-155. It bypasses the vehicle wiring so you will not have to cut and splice wiring but you will have to drill holes in the backs of the tail light housings to mount the bulbs. This is a great permanent solution if you will be towing the truck frequently.
If you will not be towing the truck that often I recommend a magnetic light kit # C-ATL20A. You will not have to cut into the vehicle wiring for this kit and it sets up quickly. Both of these light kits have a 4-Way flat connector.
Most states now require supplemental braking on the vehicle being flat towed. One of the easiest systems to set up and use is the Even Brake, # RM-9400, proportional system. It applies the trucks brakes in proportion to how much the RV is braking. This is the safest way to stop and it reduces wear and tear on both vehicles.
I have included a couple of helpful links on flat towing for you. Be sure to consult your truck owners manual for the proper flat towing procedures.
I have included a picture that shows the typical location of the factory connector on Toyota vehicles that use brake controller wiring harness # 3040-P.
The factory connector should be located underneath the dash, to the left of the steering column, taped to another harness near the emergency brake pedal. However it is possible that it could also be behind the kick panel to the left of the emergency brake pedal.
I have also heard that it can be more towards the center console hidden above a large black air duct and that you will have to reach up and feel for it. If you find it here there is not a lot of space but should be enough to plug in the 3040-P harness.
For the factory roof rack on your vehicle and the Thule Flat Top ski carrier you will actually need Universal Mounting Kit, # 7533998. This kit was designed exactly for what you need; attaching the carrier to a factory rack.
You can get replacement keys. I would need to know the number on the face of the lock to recommend the correct key.
The Titan adapter # T4845900 will work with the factory integrated brake controller in your 2008 Ford F-250 as long as you are using the BrakeRite SD system, # T4835700, and disc brakes. Or use BrakeRite EHB # T4813100 with the same adapter for disc brakes.
For drum brakes use BrakeRite EHB, # T4822500, which requires a different adapter, # T4846000.
I have included links to a couple of helpful articles on the parts needed to add electric over hydraulic disc or drum brakes to a trailer.
The holes that are on the Electrical Quick Connect, part # DL24085, can be used for mounting. You would need to make certain that the polarity of the wires you are using are lined up correctly and also need to make sure the hardware you use is the correct size so that you do not damage the connector when mounting.