Hi everyone! This will be my first post here! Sorry its a diagnostic question. I am also sorry in advance for only now starting to take serious care of my bike after one year of riding. I want to begin the learning process and it starts with diagnosing the following issue:
My 2003 savage has 4000 miles on it. I have seen it through one full year now, changed the rear tire (clumsily) by myself, changed the air filter and routinely used carb cleaner in the gas. That is about all of the maintenance I have personally done.
about a month and a half ago, my bike started to have trouble accelerating from first and second gears after letting out the clutch. It makes a rhythmic clunking sound, doesn't get up to speed very quickly and the bike jerks forward as the rhythm increases and the engine gets up to speed. I assumed it was because I had a passenger so the bike was struggling under the weight, but it was happening with just me on it later. I can stop it from doing this by very very slowly increasing rpms while letting out the clutch but it is far too slow to be practical.


As for the possible causes I can give, the most egregious is that I ran this bike on very low oil for an extended period. Oil levels are back to where they should be. I also found the fuel line had a very large and almost invisible crack running down its length. I have no idea when that appeared but I changed it and the problem persists. I also changed the spark plug, used carb cleaner in the gas and changed the air filter, hoping for a simple fix like a bad fuel to air ratio or bad spark.

Thank you genuinely for any advice or knowledge you can share about this issue- I hope I can start to ride more seriously and safely after this, so long as I didn't screw up my engine...

I really can't tell anything from the video.  It doesn't appear the low oil created a terminal failure......it may have created some premature wear on the cam/rockers/piston/cylinder.  The only way to know for sure is to ride it and put some miles on it.

You have not stated how often you ride it....and if the bike has sat for any length of time with fuel in it - or if you still have the original vacuum operated fuel petcock.

I suspect you are having fuel flow or dirty carb issues.

The diaphragm in the original petcock is prone to failure and they either leak or get stiff and stop working.....symptoms of failure can vary widely.  I would begin by replacing the stock petcock with one from the Yamaha Raptor (get the official Yamaha one and not a Chinese copy).  Look for the white box and part number to be sure you are getting a Yamaha part
LkAAOSwmfhX4r09&amdata=enc%3AAQAIAAAA0BIvtCTWWW4DmaJaoQTJSLW2iLsIFja84udjP3MOp%2F4lbvZ1Yj3K5rm47XEHzP35NZ%2BH8rSHS5H3CqlWkhpssMNYC0ycROkBN6u6Ww5B4O62gG%2F%2FXfXGiGEvf4sNYA3YhtfbTFFnm%2FzHiFyVePUcEbOjxWaSl6vPVqQoDZ3wwEc%2B2et4cSdrnVU2RNIQ5uyU5JqtqfBrSQfM21jagLxo81QQ9x5aBy2ONvtUH896doWePgjKezG7y8Z1dPL9A7Wg2luqAqmaBQg9epjAMIgTd9o%3D%7Ctkp%3ABk9SR4Ckpp_zYg" target="_blank">https://www.ebay.com/itm/273472354220?fits=Model%3ARaptor+660R%7CMake%3AYamaha&hash=item3fac38f7ac:gLkAAOSwmfhX4r09&amdata=enc%3AAQAIAAAA0BIvtCTWWW4DmaJaoQTJSLW2iLsIFja84udjP3MOp%2F4lbvZ1Yj3K5rm47XEHzP35NZ%2BH8rSHS5H3CqlWkhpssMNYC0ycROkBN6u6Ww5B4O62gG%2F%2FXfXGiGEvf4sNYA3YhtfbTFFnm%2FzHiFyVePUcEbOjxWaSl6vPVqQoDZ3wwEc%2B2et4cSdrnVU2RNIQ5uyU5JqtqfBrSQfM21jagLxo81QQ9x5aBy2ONvtUH896doWePgjKezG7y8Z1dPL9A7Wg2luqAqmaBQg9epjAMIgTd9o%3D%7Ctkp%3ABk9SR4Ckpp_zYg

I would also suggest a carb cleaning, rejet of the carb using a #50 pilot jet and a #150 man jet, and to remove the white spacer on the carb needle and either sand/file it down to 1/2 thickness or replace it with 3 machine screw washers.  I believe the washers are #4 machine screw size and they need to be steel - as the brass ones are made with too large of an OD and won't fit inside the slide recess hole.  You will need to adjust the fuel/air mixture screw for best idle..start with 1.5 turns out from lightly seated and adjust as necessary for smooth idle.  You will need to drop the idle rpm down to adjust the screw - then when you get a smooth idle turn the rpm back up to 1,100-1,200.

...and check that the front drive pulley hasn't eaten the drive splines.

You've heard from some real experts on this forum, but I'm curious what carb cleaner you're running in your fuel. It's not something routinely needed, and I've heard some of them can actually build up a varnish or something. Stab-bil isn't really a cleaner, but more of a fuel stabilizer. Seafoam has performed well for me in the past, but I only used it occasionally.

Ohio has a good point.  I missed the part about changing rear tire.
Recheck your work.

It sounds drive related to me.

Alright everyone, I looked over all of your replies and advice which was invaluable! Thank you so much for taking the time to help me. Those of you who had your bets on the belt being the problem are the winners. As some suggested, I needed to recheck my work on the rear tire change. The problem was that I didn't tighten the belt enough and it was hitting part of the metal frame just behind the front pulley. Every time I engaged the engine and sped up, the belt likely had too much leeway to move and was slapping the metal and causing the jolting and clanging noise. Incredibly simple fix and I got to learn how to inspect the front pulley, test the belt tension, use the tension bolts to tighten the belt, remove the gas tank, change spark and a whole host of other important maintenance skills all in service of figuring out this problem. Again, thank you all for putting in the time and effort to help me.

To all those who happen to have the same problem, allow me to fully detail the symptoms of this particular issue:
I had recently changed the rear tire of my bike and unknowingly made a mistake by not fully retightening the tension bolts (the bolts coming off of the flat, two planed clasps that are on either side of the rear axle)
after a month or two of riding, the bike began clunking predictably immediately after letting out the clutch and engaging the engine. This caused a jolting, slow acceleration into first and second gears. at higher speeds the jolts aren't noticeable.

I learned what the problem was when I jacked up the bike and felt the belt drive skim against metal when I pulled it.

The solution is to tighten the tension bolts on both sides of the axle. This forum has guidance on this very simple process if you need it.

Hopefully this thread can help some other inexperienced riders and mechanics!

Great news.  Your OP read like a crime scene and they say "The criminal always returns to the scene of the crime."  We just nudged you in the right direction.