Rebuilding motorcycle after timing chain skip 62K Km

I replaced the valves because they were bent. New seals too. Valve seats were reamed by a machinist who also lapped the valves although I told him not to because I don’t know if they were hardened. Sometimes they think they know better.
 
Waiting for gasket kit, sharing accessories.
 

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Tools…
 

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Trying to fit the drop link alignment pin, just playing with tools. Surprise. The drop link looks offset. The alignment pin’s head fits very tight into the large hole but doesn’t align with the smaller hole. From the opposite side the shaft fits quite loose, there’s enough play to feel it. Now wondering if I need to loose and realign the drop link too. With this bike it seems the more you dismantle the more you get to fix.
Second thought: maybe is meant to be like this. The manual says to pull diagonally back and up when installing the drop link. Maybe that’s to ensure the bolts shafts seat firmly the surface of the holes when the bike stays on its wheels under own weight… and the joints don’t move. Anybody went this far yet?
 

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Details about installation. Assuming linkage positioning procedure is meant to ensure firm contact between assembled members which have clearances. I think it’s very important during major rebuild because it’s almost impossible to check if the installation is performed correctly so components positions serve the purpose. The manual explains steps but doesn’t explain their purpose so there is the risk that some operations performed blindly by the book can still result in troubles later.
 

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I thought about leaving the barrels in place and just hoping that the old gasket will hold. Dealer’s mechanic suggested that’s not the best choice. I guess he’s right, especially when these jobs are done first time by an amateur.
Finding best practices about rebuilding engines with removable cylinders blocks wasn’t easy. Below few links showing rebuilts by fitting cylinders from the bottom of the barrels
Hayabusa cylinder block install
Suzuki GSX 1100
Honda CB750Honda CB750 barrels uneven low
Yamaha XJR1300
One note about rods side loading: best practice seems to be to level pistons first, lower barrels slowly then engage dowels. Now thinking if I need three sleeves. Or maybe side loading is more theoretical and one sleeve would do.
 
Liners need to be removed, cleaned, resealed and held down with bolt and washer so can't move. Best advice buy/get an engine shop manual.
 
Liners need to be removed, cleaned, resealed and held down with bolt and washer so can't move. Best advice buy/get an engine shop manual.
I have two versions of the engine shop manuals and a subscription for Triumph’s online one. There are no liners. Only a cast monoblock with three big bores; maybe with Nikasil, maybe not.
 

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I would think about buying a used engine
I have already a used engine . Taking into account the asphalt I found and cleaned I reckon mine’s better. It seems this tractor needs deep cleaning on a regular basis. I am also thinking about flushing the engine and open it every 60000 Km. The design is annoying because once yo need to work on the head then you need to peel it like an onion and it’s **** expensive. I am seriously considering different bikes for the future. But once rejuvenated and well maintained this one will run until it melts down. I will experiment with additives too.