2002 VFR 800, bogging/stalling mystery

So I’m the proud new owner of a 2002 VFR 800, in red!
The bike was garage kept and looks immaculate; it has 45,000 Km on it.
The previous owner didn’t ride it much last season and it was sitting in the garage over the winter, not on a tender and no fuel stabilizer.

The mystery I am trying to solve is the bike is bogging down at idle, revs are dropping well below 1k to ~800 or so and the bike seems like it is stalling out. Getting on the throttle and revving it up to 4k will keep it running but below 4k is very unstable.
This happens with the bike in gear and neutral, with clutch in or out.
I think it is bogging when the fuel tank is low (two bars), but can’t be sure if that it is consistent.

Since buying the bike I have done the following work on it:
-Oil filter (Honda oem) and oil (10-40 full synth motul) change.
-Bled and cleaned clutch fluid and master cylinder.
-Bled front brakes.
-PAIR mod (problem was present prior).
-Flapper mod (problem was present prior).
-Front and rear CCTLs (tomorrow).
-Idle adjusted to ~1250rpm.
-Three tanks of fresh gas, the most recent one with Seafoam.
-Inspected gas tank when low, looks clean with no rust or sludge that I can see.

Any thoughts as to what to pursue next?

 

First you might want to run some fuel system cleaner through it such as Seafoam. You don't know if the PO treated the tank. That will help freshen the fuel system up.

Then you will want to crank idle up to about 1350 instead of 1250.

Finally, give the throttle body a good sync all the way across.

I bet that takes care of most of your problems

 

Hey, thanks for responding!

By throttle body sync do you mean what the service manuals refer to as "starter valve synchronization", it appears to be the same thing correct?

I'll give that a try tomorrow.

 

No problem. That is exactly what I'm referring to doing. It made a huge difference in mine and it isn't all that hard to do. I highly suggest picking up a long (20+ inch Phillips screwdriver) for the insulator clamps that hold the throttle body on.

Post your results and findings too so that we can help if that doesn't fix and we can keep giving good information if it does

 

Hmm, it’s been an interesting week working on the bike. Lots of issues worked on and sorted out, this post is mainly focused on the bogging/stalling issue however.

So, last weekend I changed the CCTLs which was actually super easy to do.
Both of the old units seemed none the worse for wear. The rear unit was hardly extended at all, in fact the locking tool wouldn’t stay in due the tensioner being already fully compressed.
I started on syncing the throttle bodies only to discover that my vacuum gauge fluid was all gummy and non functional, new fluid is ordered and should be here next week.

This weekend I re-enabled the pair system, (I had just disconnected the electrical connector) and replaced the air filter which was quite dirty.
Simply disconnecting the pair electrical connector was causing the bike to run super rich and with terrible gas mileage, re-enabling it fixed this. At some point in the future I will probably fully remove and block off the pair system, for now I will just leave it stock.

Where I’m at now:
The bike is still bogging/stalling at idle/low RPM.
This only seems to happen when the fuel level is down to 6.9L (1.8 US Gal)!
I went for a long ride today, ~150 KM, in traffic, twistys, stopped several times.
All was good until my fuel level was down to the above mentioned ~7L remaining and BAM, bogging and stalled out on me.
This has happened consistently on the last four tanks of gas!

My gut is telling me this is a fuel system issue. Something that only comes into effect when the fuel tank is low.
Bad fuel filter? Bad pump (oh gawd)? Bent pickup tube or something?
Thoughts from the hive mind…?