*Note: I'm not a total noob to bike mechanics but I am by no means an experienced mechanic.
Bike seemed to be running fine for the last week or so since I bought it. Nice acceleration, good sound, etc. No issues whatsoever that I could tell. Went to start her up yesterday morning and the battery was noticeably drained, she tried to turn a couple of times, didn't start, and then I just got clicks. Pulled out the battery and hooked it up to my DuraBoost 750 I got from Cycle Gear. Now, this was my fault as I didn't let the battery charge all the way. Let it go for about 2 hours, unclipped it, and she started right up. Drove around a little bit, no issues. About an hour later, left to meet my g/f at the dog park and the bike showd some signs of drainage but started up. Got almost there, stopped at a stoplight, I noticed when revved the throttle hard, it wanted to die on me. If I rev'd real easy it would rev up but if I hit it hard, it would rev down and almost die. Pulled into a parking lot, played with it a few times like this and it eventually died. Wouldn't start, just clicks. Got her home, noticed this time that battery levels were low. Got some distilled water, topped it off, and this time let it charge overnight. (While it was charging, I tore down a few other areas of the bike, which I think is the cause of this problem, which I'll get to in the next paragraph.) This morning I had the green light on the charger, she started up like a beaut and has been running all day except now, I have a different issue. The engine/exhaust (not sure which, maybe both) seems to be somewhat muffled compared to how it should sound. Also, I have a noticeable loss of power. The bike runs, and it will still get up and go, but it's less powerful and there's a kind of muffled sound to it. I kept revving the engine, listening, thinking it was just me but now I'm sure. It sounds different. A muffled, almost deeper sound. I think I also hear or feel more vibation/rattling but that might not be the case.
So, last night, since I had the battery out charging, and I had done some research about the FZR's voltage regulator issues, thinking this might be my problem, I decided to tear down the rear panel and check out the VR just for a quick visual inspection and to get an idea of what I'd be doing if I decide to or end up needing to upgrade to the R6 VR. I took off the VR, looked at it, observed the wiring pattern etc, and re-installed it. After I did that, I decided to tear a couple of other areas of the bike down just for familiarization and some preventative maintenance checks. This is where I think I caused something to go wrong. I removed the tank cover, and removed the intake(?) cap piece that covers the air filter. I pulled out the air filter and noticed it was pretty nasty and is going to need to be replaced. I put it back in, and screwed the piece back in that covers the air filter and compartment. After riding today and noticing the muffled sound and loss of power problems, I immediately assumed I must've caused a problem somewhere in this compartment, or in the air filter itself. It just seems to make sense with the loss of power, muffled sound. Like maybe air is escaping or seeping out or being prevented somehow from getting to the engine.
Just 20 minutes ago whein I took the tank cover off and pulled out the air filter, I noticed a few things. One, the rubber gasket that sits inside that cover/intake piece you remove to access the air filter - wasn't fully seated. 1/3 of the gasket was hanging out of the groove it should've been in. I'm not sure if I put it in like that last night or it came out just as I took it off just now. I'm assuming I most likely put it in like that last night not noticing. If that gasket wasn't seated, could that have caused air to escape and cause the issues I'm having now? I forgot to get a picture of the gasket out of position and I already put it back in and now I can't seem to get it out to get a picture to show you what I'm talking about.
Now, normally I would just put it back in with that gasket fully seated and start the bike and see if that fixes the problem, right? However, after I fixed the gasket, I noticed that parts of the air filter were just covered in what looked like a dirt/sand mixture (I live in Florida). I'll post pics below. I got out some Simple Green and began cleaning. It was really sticky and hard to get off. Thus, I started thinking it wasn't dirt/sand, but the remnants of an old foam cushion/gasket or something. And now I took it all off. Which brings me to my next question. What was that? I'm afraid to put it back in and start the bike now for fear that that was a necessary, albeit filthy, filter gasket of sorts. I might have to wait until tomorrow or maybe longer to get an air filter ordered if the cycle shop doesn't have them in stock. (Auto parts store can order them but that takes a day or two.)
Then again, maybe that gasket had nothing to do with the problem. Could it have something to do with the battery situation? Maybe the VR is bad and now causing electronic issues with the way the bike sounds and runs? I'm at a loss. That's really all I did last night though. Pulled out the VR and mount, put it back in. Fully charged the battery. Pulled out the air filter, put it back in (possibly leaving 1/3 of that gasket not seated).
Here's a pic of the air filter/cabin cover. You can see the gasket is in that rim where it's supposed to be. About 1/3 of it was hanging out when I just pulled it off.
Here's the inside of the cabin with some remnants of the foam gasket stuck to it.
Here are some pics of the air filter with that gunk/foam crap on it before I cleaned it all off.
Any ideas?? Is it safe for me to start the bike after having cleaned all of that foam off of the filter? Or should I just get an air filter before trying to start it up again? I was just about to do an oil change, spark plug change, and coolant flush, since it probably hasn't had one in a while. I realize that perhaps multiple things could be causing this problem but it seems odd that right after I messed with the filter is when the bike started behaving differently.
Any help or ideas would be much appreciated. Thanks!