What does this knock sound like to you?

[turbosteve84]

Could it be the balancing shaft?. I was ready to "button up" my alternator cover when I thought I'd give the internals one last look to see if everything was properly in place. Checked the manual, and saw that there's a "dot" on the balancing shaft gear that had to align with another "dot" on the flywheel gear (?)

Sure enough, I had failed to align the gears!

Check the manual (it's a free download here somewhere), and look for the balancing shaft alignment.

You should tighten that flywheel nut properly. I have a 46mm deep socket that I could lend to you. Probably about $5 to ship to Alaska and another $5 for you to return it. Or you can just order it from Sears. I think it was about $23 with shipping (see attachment)  --Steve

[akvision95]

Just a quick status update: took apart the bike some more today and when I removed the air filter cover, there wasn't one inside! It's possible the PO ran the bike for like 3-5k miles without the filter in because when he sold it to me he said it was something I should check because he hadn't. This seems like it could have messed up the carbs and the engine both.

Additionally, removed the oil filter again today in preparation for disassembling the right crankcase and found that there were both gold and silver colored metal shavings in it but not as many as last time.

Later tonight I'm planning on removing the right side crank case to see if there's something going on there.

[fret not]

 RH engine cover houses the water pump, the primary drive, clutch, and shifting mechanism.  In this cover there is a small oil seal that should be replaced as it keeps oil and coolant from getting mixed.  PN# 93101-14098-00  It's held in place with a circlip.

[akvision95]

Opened up the right side crank case today and didn't see or feel anything that looked obviously wrong. So I'm going to keep digging deeper into the engine, try to figure out what's wrong in there. Planning on dropping the engine out and completely disassembling it.

Might be looking for a new crankshaft or some connecting rods in the near-ish future... unless it's damaged beyond repair

[lexx790]

I had my crank reground with new bearings over 5 years, ( 15k miles ) ago and still going strong.

[akvision95]

Alright so I got the heads, cylinders, and pistons off today. The rear cylinder connecting rod is super loose so its probably the bearing? But the front one is absolutely fine and feels great. Going forward, is there any way to replace the bearings without splitting the crank case? And should I replace both or just one of the bearings? How do I know if the crank needs to be reground etc?

[fret not]

You really need a shop manual for step by step procedural guidance.  Yes, the cases have to be 'split' to access the rod bolts.  Do some serious searching on this site, Motoracer8 has some experience and sage advice in this regard. 

[akvision95]

I have a shop manual and have been following the directions in it. Reading ahead a little bit today and I was wondering where to get all the gaskets, o-rings, and piston circlips etc. Is there somewhere I can get all the parts at once instead of looking for them on eBay piece by piece? I only have a month to finish the rebuild so it would probably be good to have everything (or as much as I need).

[The Prophet of Doom]

I got my full engine gasket kit from Wemoto.co.uk 
This has many o-rings and seals in it as well, but not quite everything you need for an engine teardown. Expect to source bolts, circlips, waterpump seal, bearings and worn engine parts separately.

[fret not]

I suggest you get as much as you can from a Yamaha dealer for the parts that are available.  The rest of the stuff you get where you find it.  Look at a parts fiche and write down the part numbers you need, then go shopping.

More information on rod bearings should be found in past discussions revealing what cars they fit.  The "Clevite 77" brand is the recommended rod bearing material, and you will probably have to order them from an auto parts shop or machine shop that does automotive work.

[akvision95]

Should I just buy a new crankshaft given the sounds my bike was making and the wobble in the connecting rod? Or is it possible that the crankshaft might still be good even with how bad it was sounding and all the metal shavings?  I haven't gotten a chance to open up the crankcase yet but will hopefully be doing that tonight.

[lexx790]

When mine went it was similar to yours with only the back one slack.
I was worried about regrinding the shaft with regards to the surface hardness, getting shell bearings etc.
Took the shaft and rods to a local engine machine shop  and had it reground and fitted with Austin mini shell bearings with a tiny bit of modifying.
The shell bearings were cheap easy to come by in UK and had a range of sizes with -0.010" to -0.050".
Cost me just over 100GBP.
And like I said that was over 5 years ago and still use my bike to and from work every day.

[akvision95]

Okay good to know.. I was thinking about just picking one up on eBay because there's a nice looking crankshaft for $20+shipping. Also I talked to a couple machinists in the area who said that nobody here really does crankshaft resurfacing, so I'm not sure if that would even be an option. Basically what you're saying though is that a bad knock like I have indicates damage to the crankshaft that would need to be fixed somehow, whether by new crankshaft or regrinding, right?

[fret not]

The rod journal on the crankshaft is pretty hard and sometimes needs little more than a good polishing, though it CAN suffer scoring if metal particles become trapped between the bearing shell and the journal.  In the latter case the journal needs to be ground smooth.

I think the knocking sound comes as the big end of the rod distorts slightly and bearing material gets worn away.  This leaves a bit of a gap that allows the parts to slap against each other as they transition from push to pull, and back again.  The damaged rod often needs to be 'resized' before reusing it.  A small amount of material is removed from the mating surfaces of the rod cap, then it is bolted to the rod and precision reamed back to correct size for the journal.

[dingleberry]

... is pretty hard and sometimes needs little more than a good polishing...
... a bit of a gap that allows the parts to slap against each other as they transition from push to pull, and back again.  The damaged rod often needs to be 'resized' before reusing it.

Geez Fret, take it easy. Think I need a cold shower  :o

[fret not]

"New" crank on eBay may not be any better than the one you already have.  And there is no way to know about the crankshaft you have until you take things apart and actually measure the parts.

[akvision95]

Any tips on rod bolt removal? Do I need to heat it up or use an impact gun or something? Can't seem to get them loose.

[dingleberry]

Use a long breaker bar. Don't hit them with a hammer or suchlike as you don't want nicks, dents or scratches on your rods or caps.

[dingleberry]

I see you said bolt oops! Do you have access to a press? You probably can use a big vice set up with hollow dowel to push them out until you can tap them through with a hammer and wooden dowel. Be careful things don't slip. As I said above you don't want to mar the surface of parts.

[akvision95]

Meant nut whoops. Is it okay to use an impact wrench or not?