With the suggestion of others, I will re-open this thread and wrap up my bike's engine overhaul experience and thus helping to contribute to the overall knowledge base of the motobrick.
I bought some used connecting rods/pistons on ebay from a parted out 1994 motor with 30k miles. It is important to note that the rods in the "newer" 1990's bikes are lighter that the ones from 1980's bikes. And you should not mix and match but rather find connecting rods from a similar year bike.
I pulled the cylinder head (and everything else that it took to actually pull the head) and crankcase cover. I only extracted the one offending rod from the engine. (number 3) I left the other two connecting rods/pistons in place. I removed the the connecting rod bolts and slid the piston/rod out the top end of the motor. The crankshaft was left in place, (and the two other pistons as well) I know that work is done to get the pistons/rods to be within a similar weight envelope. I weighed the old connecting rod on a postal scale and then the donor rod. They were almost exactly the same weight. I considered myself lucky in that respect.
I elected to re-use the old piston from the bent rod. I couldn't find any defects and was concerned with the weight balance issues and wear pattern in the cylinder itself. I attached the old piston on the new (donor) rod using the donor piston pin and clips, and started the process of re-assembly.
While the cylinder head was off of the bike, I took it to a shop that does cylinder head refurbishments. I just wanted the standard treatment, dunk tank to clean out the old carbon deposits, make sure the head wasn't warped and make sure the valve seats where good. One note about the cylinder head removal/installation. To remove the cylinder head, you have to remove the camshafts. And to remove the camshafts, you have to remove the cam sprockets. Be sure to keep track of which sprocket came from which camshaft, I even kept track of which cam sprocket bolts came from which camshaft (intake or exhaust)
My most OCD task was making sure the connecting rod was attached to the crankshaft correctly. I was using the bearing inserts that came with the donor connecting rod. I torqued, the loosened and then re-torqued the connecting rod bolts to make sure it was correct. In mounting connecting rods, you want to make sure that a thin film of motor oil is on the crankshaft surface and on the bearing insert. Since the crankshaft was still in the motor, I was concerned that I would not catch any binding of the connecting rod. So I rotated the crankshaft many, many times with a torque wrench, making sure that I was using a consistent amount of torque through out.
Assembly was pretty the reverse order of disassembly with new gaskets and other rubber bits. I checked the valve clearances with the cylinder head on the bench (camshafts in place) and made a couple of minor adjustments.
While everything was apart and I was waiting for shipments to arrive, I had the injectors cleaned, (Mr. Injector) cleaned the engine block, air box, clamps, in short, everything.
With every back in place and new oil and coolant, the moment of truth came to see if it would start up. It took enough cranks to get the fuel rail pressurized then the motor fired right up. Oh sweet joy.
But over the next couple of days, the bike continued to backfire occasionally and the number 3 cylinder was still running rich. It was returning to it's former ways. (the spark plug was wet with fuel when pulled from the engine) So even though I fixed the bent rod, there was still some other issue that I had not yet resolved.
I discovered the problem (and resultant solution) when I decided to perform a throttle body sync. When I pulled the vacuum line from the number 3 throttle body to attach the Carbtune, fuel came dripping out of the vacuum hose. That vacuum line goes from the number 3 throttle body to the Fuel Pressure Regulator. This was the "ah-ha" moment. I had a bad fuel pressure regulator, a very rare condition. A condition that has not been discussed here on Motobrick.com. I'm guessing that the diaphragm in the FPR started to leak and was allowing fuel into the vacuum line.
If the engine stopped when the piston was drawing in fuel/air mixture, that would also drawing in a fair amount of fuel from the FPR vacuum line. Then when the engine was started, that excess fuel would be trapped on the compression stroke resulting the aforementioned hydro-lock and damage to the number 3 connecting rod. Remember that the 1990s vintage connecting rods are lighter than their heavier, beefier 1980s versions.
I replaced the Fuel Pressure Regulator, synced the throttle bodies and I haven't looked back. The engine has been working flawlessly since then. I consider the problem fixed.
