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Let's rebuild this bike, a 1985 RZ350N.

It was left out and has a rusted tank, plus the motor
is full of emulsified oil.

The first step will be to remove the engine from the frame.
Drain the transmission oil. Remove kick starter, shifter, fuel line, side covers, tank, chin cowl(and catyverter stuff, if still there), pipes, cables, battery, and a tip here is to remove the Tacho cable BEFORE the carbs, manual blows off this step till later.
Drain coolant by removing radiator cap, water pump hose, and cylinder drain plugs.
Remove plug wires, thermo-sensor lead, and upper radiator hose from head. With the carbs off the clutch cable can be removed. Plug the oil line to the autolube tank. Remove left engine cover. Loosen front sprocket and flywheel nut while locking up rear brake in 2nd gear.
On this bike the rear brake master was rusted solid, so I used a lead fishing weight between the chain and sprocket. Remove the right side clutch cover(water and oil pump remain in cover) and loosen the nut on the primary gear,now is the time to remove the clutch too, put a grease pencil mark across the plates, basket and cover so they all go back in the same position.
Dissconnect wiring harness/plug and mark them. Remove front, rear, and tension rod mount bolts(under engine), and have someone help you lift it out sideways from the right side of the frame. Set the engine on a piece of cardboard, plywood, or a folded newspaper to protect it during teardown. Whew! I need a beer now, how about you?

Take a look, this is where we are at, this weekend the engine gets
torn down.

*Clean engine before removing.
*Drain oil prior to removal.
*Remove Tach cable from engine before carbs.
*Lock up chain with brakes or lead to loosen sprocket nut, and center clutch boss.
*Lock up crank and clutch basket with a rag or lead in between the gears to loosen flywheel, primary, and clutch basket nuts.
*Use boxes to put the covers and engine bits in, use plastic bags to keep bolts/bits organized.
*Put a witness mark on the clutch assy.
*Use a flywheel puller, it's the only way to do this without damaging bearings and cases!

I had to used my neighbors 1/2 inch air impact gun and a 32mm socket to get the sprocket and clutch hub nuts off, everything else came apart by the book, using a ratchet or end wrench.
The cases are apart, and we found that 5th pinion and drive gears were bad, as well as a bunch of "C" clips on the tranny shafts. Someone put an RD400 5th gear in and it allowed the tranny to go into 2 gears at once with some crunching of gear teeth.
Cary and I went through both shafts using the manual to verify the sequence, orientation and type of gears and parts.
A BIG thank you to Cary Behar of RZs Unlimited for helping me do a hands on rebuild of the tranny gear clusters, he is THE MAN on these. The crank and all bearings survived the 5 year bath in emulsified oil, and we rinsed them off in Diesel fuel filled pans(the cheap disposable aluminum pans sold in the grocery store).
The primary gear had a groove in it where the seal went so Cary set us up with a new one and told me this: A neat trick is to fill the keyway and inside of the primary drive gear keyway with silicon seal prior to fitting it back on the left end of the crank, this seals the gear to the bearing and shaft.
MEK removes old Yamabond from the case halfs(get'em perfectly clean). I used spray Gunk Engine Brite to clean up the cases, get out the toothbrush and scrub that grime off! Then rinse off with water and blow dry, now you can paint/touch up the top case, I used gloss black.
I honed the cylinders, and cleaned the pistons, head and powervalves of carbon deposits. Be sure to have new folding washers for the clutch and sprocket, and a new O ring for the waterpump outlet pipe.
I replaced all crankcase seals as well as the water pump, kick starter, and oil pump seals in the right crankcase cover.
The pictures will follow, right now they are being developed.
Re- assembly of the cases is next, till then so long, Jayman.

Engine/Case dissassembly: Remove head bolts in reverse order(10-1). Remove head, if stuck, rap lateraly with 4 lb dead blow hammer.
Loosen and remove the two screws on the power valve coupler between the cylinders. Remove cylinder nuts(4) on the left side, and remove. Lift off the cylinder. Repeat for right side.
Place a piece of hard wood in the exhaust port to block power valve and loosen hex screw to uncouple the power valve halfs, now remove the retainer allen bolt and retainer and remove power valve.
Pop out the outside piston pin circlips. De-burr the groove in the piston(an Exacto #11 blade with tip broken off will do). Place one piston @ TDC and push out the piston pin using a 3/8" socket extension, repeat for the other side.
Place a rag between the primary and clutch gears and loosen the nut on the crankshaft, remove the oil/water pump drive gear and primary gear.
Loosen the six clutch spring screws and remove hub with plates in one piece, set aside. Flatten locking washer with a punch, and remove clutch basket retaining nut(32mm), an air ratchet set on medium reverse @125lbs is perfect for this. Repeat for sprocket if you forgot to do this prior to engine removal, it's 32mm too!
Take out the two phillips screw bolts holding the clutch(pinion) shaft bearing retainer, and set them aside. Now loosen the case screws in reverse order(16-1) starting with the top case screws, and then removing the bottom case nuts. Take that trusty dead blow, and smartly wack the front and rear of the cases, remove the top case.
Ponder for awhile!

1-12-00 UPDATE: The tranny and cases being full of milky emulsified oil, we prepared some aluminum foil baking pans(disposable) by filling them with diesel fuel, and immersing the shafts in them while scrubbing away with a stiff tooth brush, and did the same for the crankshaft and other bearings/ components. Cleaned up the cylinder after honing with WD-40 as a lube. Ditto for the head and clutch cover..get 'em clean. Rub the pressure plates on a flat section of sidewalk enough to roughen them slightly with crosshatch, don't round the edges though! A light de-glaze of the friction plates( just enough to scratch the surface) can be done too. After the diesel fuel evaporares lube all shafts and bearings with Yamalube and check for roughness while rotating...if so it's off to the machine shop! We found a busted 5th drive wheel and the wrong(rd400) mating 5th pinion, this caused the bike to go into 2 gears at once and broke teeth and dogs, what a mess. The primary drive gear on the crank had a deep groove where the oil seal lip goes, so it was replaced. The pistons cleaned up easily and measured within tolerance, the cylinders also cleaned up well from honing and were in spec., so they were re-used as is. Amazingly, the crank also survived. After removing and replacing all the bad gears and bent circlips on the shafts the cases were cleaned of Yamabond using a rag and MEK. Lube all seals and shafts with grease and carefully slide seals on shafts with letters facing outwards. Drop in the drive and pinion shafts into the lower case, align with shift forks before seating. Repeat for crank, being sure seals stay in position. Apply a bead of Yamabond 4 or Three Bond #1104(samo samo) to both case halfs, and spread with finger of brush, do not get ant into the oil holes for the crank ball bearings(or clean it out with a Q-tip). Double check the shifting and smooth rotation of all three shafts before dropping on the top case, and be sure the bearing anti rotation pins and rings are in place and in their respective notches too. Now drop on the case and seat it with a tap of the mallet front and rear, it should close up, if not, something(like a pin on the crank bearing OD) is not lined up, take the case off and fix it. Fasten cases with nuts and bolts following the numbered pattern on the cases, then torque in 3 stages per the the Yamabond ooze. Next we will put on the top end, and toss it back into the frame.