FI light coming on and off while riding accompanied by RPM surging and backfiring

Hey all, I was in my driveway getting ready for a ride and as soon as I started moving I noticed the FI light and a bit of jerking from the bike. It went off so I assumed it was just a weird one-off quirk that might have happened due to the cold. But as soon as I started going down the street, it would intermittently come on and the bike would run like absolute crap, RPM surging and excessive backfiring. This continued even up until when the bike was at temp. Eventually, it was getting so excessive that before I even made it 3 blocks away I had to come back. At certain points I could've sworn the engine straight up just shut off.

Now, for some background, this is a 1999 VFR800 with 80k miles on the clock of which I am the third owner.
This was sort of out of the blue for me. Now looking back I feel like very low speed in 1st gear felt like it was lugging? As if I had to slip the clutch for a while until it was smooth. But then again, that might be the way its supposed to be. Another thing is the bike did overheat once 2 months ago when I brought it to 255F momentarily before I pulled over and shut the bike off (that time I was just low on coolant), so it might have triggered R/R (SH689DA) or stator issues on my bike.

About a month ago, it seemed like the battery wasn't really holding charge well because it had died on me and I had to push start. I went on an 80 mile ride and only three days later the resting voltage on the battery was at 11.95V. Since then I always keep it on a trickle charger until it reaches full charge before I ride(~12.7V). So at the time when all this FI junk was happening, my battery was at full charge. I must also add that while checking the battery with a multimeter, I saw 13.65V at idle and 12.45V at 5k rpm.
Ever since the battery thing I suspected either it was just the battery, or maybe the R/R was going bad and causing the problems.
I tried to do "The Drill" today (pin-to-pin check on stator side connector) but I didn't really know what I was looking at and also it was very difficult to pull apart. The sun set so I'm going to try it tomorrow.
I attached an images and I have two questions:

1. Why is there a 25A fuse in the 30A holder (not pictured here, but I found the 25A fuse with no burn marks around the holder or anything)?

2. What exactly am I looking at with this orange connector and how do I pull it apart?

I did a check for FI codes and there were none, and none when I bridged the service check connector as well

I do have one suspicion, and that is the vacuum tube to the flapper valve that I had disconnected a while back. At the time all my friend had was teflon tape, which wasn't particularly sticky. When we taped up the vacuum tube, it might have come loose since then and maybe that's causing the issue? I can't check under the tank until tomorrow because I don't have any spanners with me.


If you read this entire infodump, thank you, I'm just trying to figure out what's going on.

 

The drop in voltage as the rpm's rise is a sure sign that your R/R is shot. The other is unrectified AC passing through the R/R which melts connections and blows light bulbs!

How old is the battery? Have you removed it, charged it, then had it load tested?
These are the first items that you should check.

I suspect that a previous owner replaced the 30 amp fuse with the 25 amp because that is what he had on hand. If it is not blown that is a good thing. However, if it was mine, I would replace it with a new 30 amp.

In the photo of the orange connector I do not recognize that red two wire line behind it. Does that supply some type of accessory?

 

I'm not sure exactly what that red and white cable going into the connector in the back is, I think when I looked at the wiring diagram its just a connector that's inline with the 30A main fuse.
Anyways, you were pretty much right on the money. I had a pretty weak battery, wouldn't hold a charge very long (would drop down from 12.7V to 11.9V when unplugged for just 2 days). I'm not sure how old it was, might've been a few years. But anyways, I would fully charge it after every ride on a trickle charger. I did notice that this RPM surging issue would happen when I didn't bother to charge it. I purchased a new Yuasa YTX12-BS, but even with this fresh new battery the voltage would be 13.6ish at idle but would drop to around 12.6 at 5k rpm. This gave me a strong feeling that the R/R is not charging the battery properly and may need to be replaced (currently have SH689DA). I did end up doing stator checks, and everything checked out, except I didn't get to test it anywhere above idle. This weekend I'll do a thorough check with my friend and decide what needs to be replaced. If it's the R/R I'll need to research and find out which one to get.

 

Okay, so the old battery may still be fine, you've eleminated the battery as a potential problem by purchasing a new replacement.

You stated that you did "the drill". Did you do it the way that Mello Dude posted staring in post #9 of the following thread? https://vfrworld.com/threads/how-to-fix-common-regulator-stator-failures.39277/

The lugging at slow speed, if it is to the point of the engine almost stalling, would make the fi light come on without recording a code. What is the RPM when the bike is warm and at idle? It should be ~1200+/-

As far as which R/R to replace with, the afore mentioned thread has some very good suggestions, or just go to roadstercycle.com and check out the options one of our members here has. I did the roadstercycle direct-wire to the battery 5 years ago when I installed an FHO20AA R/R and have had no issues since. A cheap ebay voltmeter installed indicates that I have a consistant 13.9-14.3 Volts while the engine is running, and (knock on wood) the Chrome brand battery installed 4/28/2017 has continued to serve me well.

 

I had done the drill earlier but I was missing the stator checks at 5k rpm. I just did it again today with this new battery, stator is fine, R/R is looking bad because my battery is showing 12.6ishV at 5krpm.
I've decided to buy the SH847 kit from roadstercycle.com but I'm not sure about about how its going to be mounted or which mounting bracket to get for my 5th gen.