'06 FLHXI, DEVELOPED A VERY ROUGH SHAKE IN MOTOR.

I really need to know the mileage.....?..also the question isn't very clear ...Is the whole truck shaking roughly or is the engine shaking roughly or is it both the engine and truck shaking..?..Since I am not sure I will answer what I can....Ok......If the truck is shaking while sitting still at idle the engine/trans mounts could be worn and or loose mounting hardware...If the engine is running roughly at idle causing all to shake that bad it could be a number of things causing it as usual...Quite often a faulty plug wire/and or bad plug will make it have a misfire because it will be running on only 5 cylinders..If that's the case it could be more than one bad...A vacuum leak will cause it to perform in the same manner...however all cylinders will be firing..Normally a vacuum leak is easy to pinpoint..however it could be a faulty IAC valve..(IDLE AIR CONTROL)..The idle air control is designed to hold a high idle at start up then slowly bring idle down to proper Rpm.....A faulty TPS (THROTTLE POSITION SENSOR) will also cause a rough running problem..And let's not forget the O2 sensor..(OXYGEN SENSOR)..The O2 sensor controls air/fuel mixture...and yes an exhaust manifold gasket will make it run rough but not too bad...It has a rough running sound more so than causing it to horribly shake..It will shake but not to bad..
it is located at the exhaust side of engine..The exhaust manifold is mounted to the engine exhaust port..the exhaust pipe is mounted to the exhaust manifold and the muffler/cat converter is mounted to the exhaust pipe...You can check the plug wires quickly..With engine running carefully remove plug wires 1 at a time..If the sound of engine gets worse the wire you removed is good..after verifying it is good or bad plug wire back on then pull the next wire..and so on..If you pull a wire off and there is no change in engine operation that is the bad wire..If that is the case change all plugs and wires...One at a time..(It is a good idea to make sure all wires come off easily before starting engine..old wires will come apart easily..grasp wire tightly at boot and twist left to right while pulling..)as far as the other components I spoke as well as many others,the best,easy way is to have it hooked to a scanner and they can check/test all components for proper operation...Now..If it runs good but is shaking the engine/trans mounts are worn as I stated earlier..any loose engine component will cause an engine shake also but you should notice it at a glance...engine mount bolts/nuts being loose can be tightened without changing mounts if caught in time..Trans could be coming loose.also worn clutch will cause vibration...Send more info and I can guide you to remove and replace any faulty components you may find to save you money.........Brooks/Metalpoet.....

Engine mounts control the engine movement but it may be because the idle rpm is too low. Most of these cars idle at 950 -1000 rpms.

run the fault codes
check for vacuum leaks on all vacuum hoses
check fuel pressure
use quality injector cleaner

When was the last time a full tune up have been done? A bad intake gasket would do that.

Hey Chris,, you are starting a project (or wanting to) that is going to be problematic... It will be easier to go buy a new trolling motor with the money you are going to spend attempting this conversion... the newer trolling motors are so much more efficient...
Trolling Motors Fishing Motors Electric Boat Motors MotorGuide Trolling...
https://www.minnkotamotors.com/

Possible Idle air control, simple to change on the throttle body

It could be a problem with your rubber front engine mount or it could be that the engine is no longer balanced like it used to be. Check the front engine mount for cracks or any faulty condition.

Now, from the factory, the engine is roughly balanced so as not to shake too much. To do this, be weigh the pistons, rings, wrist pins. Then the factory drill large shallow holes in the flywheels to "balance" the assembly. Now,when you install the upgrade, you changed the piston size drastically and if this included a "stroker" crank, the crank may not be balanced as closely as the original. Also, the camshaft was probably changed. A more aggressive profile camshaft will cause the engine to idle just a bit more rough as well.

Stock engines are designed to idle smoothly. High performance modifications usually do result in the lose of this smoothness.

Ride Safe.
Steve

You could have a problem with the rubber engine mounts or the stabilizer links or both. It's not unusual to have a vibration at idle and up to about the 2000 rpm point on most rubber mount machines. This is because the rubber mounts are designed to dampen the high frequency vibrations at the engine speed people usually ride at, over 2000 rpm.

Now, if you've suddenly developed this vibration, I'd check the engine mounts and stabilizer links. The stabilizer links look kind of like those turn type cable tensioners. I think there are two on your bike, one up above the carb/ throttle body, and possibly one near the front motor mount.

I would ask you why you want to change the mounts? They usually are not a problem unless the car was in a crash. Can you see that they are broken? If it is just engine shaking due to rough idle then the motor mounts will not solve this. You will need to find out what is causing the misfire to smooth it out.

i may have an answer for you i have an imported v6 3.8 it has recently developed similar problem, i have been looking on www.kiatech.com whcih is very informative, there is a technical bulletin on my model (06) that refers to possibility of faulty o2 sensors which may or may not be the cause of the problem, it also gives me part numbers, check out the site look up your own model it may give you the answers
you can check out the main manuls or look up past technical bulletins (tsb)
good luck