Been chasing an intermittent stumble all spring/summer long.
No codes till this past week after buying the parts to change out fuel internals for the efi. More on that in a moment.

Bike would run well with a full tank of fuel, but with the last qaurter she would stumble and want to stall out , especially in stop and go traffic.
Top off with a full tank and she would be good to go. so after three tank fulls of this I figured it was the fuel line troubles that I had back in 2006 (my bike is an 02 btw)

After the last episode I figured it was an internal fuel line leak, bought all parts and was ready to tear into it on Friday before work when I decided to check for codes one last time as now the check engine light comes on and stays on for 15 seconds and then bike runs like a pos...

The code that came up was/is P0505(historic) loss of idle speed control. I shot some wd-40 around the intake checking for leaks , found none, so it appears I need an idle speed controller for $72.00 at my local dealer.

Returning the parts for the fuel tank internals for one of those iac thinggies.

So, I'll add the parts needed to swap put fuel lines and filter, etc...

10 of 1311D sealing screws @$1.39
1 of 10222 clamp 8mm @ $3.69
1 of 61402-02 gasket, top plate @$8.39
1 of 61001-01 fuel filter kit @ $93.95 and this should include an o ring and two 8mm clamps.
1 of 61408-00A body assembly check valve @ $76.95
1 of 62349-04f fuel line asy tank to intake @ &59.95.

I posted this for information purposes and I know these items can be sourced cheaper online but one needs the shopping list first and prices where full blown retail here in the Vancouver Canada area.
Hope it is of some use to the OP.
Rob

 

In-tank leaks can originate from a cracked or perforated hose, but also from a leak at the fuel-pressure regulator. Mine was at the base of the regulator and it had to be replaced. Like I said before, it was not the source of my stumble/misfire maladies, but it needed to be fixed since it was a problem waiting to surface. As already mentioned, change the fuel filter while in there.

 

Replaced the hose between the filter and fuel pump. Check the hose from the pressure regulator to the quick disconnect and it's fine. Checked the 0-rings and they look good, so I don't the problem is in the fuel tank. Also above 2000 rpms, the motor seems to run fine. It's between 900 to 2000 rpms where it backfires and misses, and runs like $hit. While I had the tank off, I pulled the injectors and sent them out to be checked and cleaned.

 

Did you find your problem yet? I'm curious.

 

What was the problem with the bike mine is doing the same thing now just at the lower rpms

 

Mine is too...fires up fine, idles above 1000 for 10-15 seconds and then will drop to a lovely 400-600 and eventually stall if I don't keep the throttle open just a hair to give it gas. Only does it on idle or when at a stoplight. Riding is fine though.
I checked the map on the PCIII, tweaked it, loaded a new map and still the same thing. I guess I need to search the forum and eventually tear in to this old thing...