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P.S. - opinions on break-in procedures? I figured I'd just take it easy for the first 500. 

Blitzed the head after work and managed to install the valves, torque down the head, and set clearances within 3 hours. Got too chilly before valve cover went on but I'm pretty pleased. I can't use the words I want to use, but I had a tough time removing the old upper chain guide - probably the hardest part of today.
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Tomorrow or Sunday I'm gonna spend some time with my other girlfriend but I may be able to get the bike running before Monday...though likely not rideable. Still, I'm satisfied for now. 

P.S. - anyone in the MI area down to weld my seat pan? It's got a couple cracks, and aside from that I'm thinking of modifying it to fit over the 1000 tail.

Tips on break in 
Do not run motor at a constant speed for any length of time  .  Vary rpm  as much as possible
Go for a ride  and then let it cool down , then do it again   ( thermalcycling  ) or how ever you spell it 
After  50 to 100 miles  change the oil.  Then dont be afraid to wind out the gears  but dont float the valves 
Have  Fun  

Okay, did about 5 miles so far, retorqued the head this afternoon. The aftermarket exhaust gaskets are taking a good while to crunch down so it sounds kinda bad for now. The carbs are a bit unhappy with me, having sat for 3 months, but maybe I'll get lucky and they'll clear out on their own...first time for everything. 

Special thanks to rstnick for the new keys (now they stay in when the bike is on) and calum for the breather to airbox tube (will help keep the engine a bit less oily up top!)

Also, it's probably a bit early to tell, but the Permatex anaerobic sealant I used on the crankcase seems to have worked, with the added benefit of making my engine look like a squished jelly donut. 

60 miles now after today, feeling pretty good. Exhaust leaks taken care of and timing adjusted; after I dismounted at home I heard a crash and saw a familiar scene behind me. Luckily there's no real damage - just some dirt on the mirror and a scuff on the fairing.
I suppose it's time to modify the kickstand so that it doesn't do this. I knew it would happen someday, but you know how it is. 

Still hanging a little on the revs, but not as much now. Takes a blip of throttle to start, which is how it was before the rebuild. I was hoping I'd magically get the one-crank starts of my Ninja but it's no big deal. 

Recorded a short clip of 1-2-3 pull. 


Mechanically the transmission swap is a success, and even has the slight benefit of having a much wider neutral than the transmission I took out, so it's very easy to find. However, assuming my new speedometer is as accurate as the old one (no reason to doubt it) my RPMs in 6th gear at 70mph are a little over 5500, so my fuel economy will suffer a bit from that. Oh well. It's fun, it's nice to have the same number of gears as my other bike, and it's different. 

I think my next step will be fixing the front air forks; I rebuilt them relatively recently, but the equalizing hose between them leaks, so they don't work right. I'll see about having a new hose made or try to find the thread size for a couple plugs. 

Also - not to talk up a maybe - I've been looking into turbocharging recently and it doesn't seem that complicated; I've got a large expense coming up later this year, so nothing will happen soon, but I think blow-through CVK32s would be a decent setup (since I wouldn't want to wreck my BS34s - someone else may be able to use them if I go this route)

Sounds good, pulling nice and clean...

Well, my girl's feeling a bit under the weather. Rained while I was at work on...Friday or Saturday, and was firing on two with the tachometer not showing. It would come and go, and going full throttle would wake it up a bit. 

Happening again today at work and it's bone-dry, about 85 degrees. Popped in some new plugs and a main fuse but no dice. Wiggled all the wiring connections and it's not entirely gone but seems to be a bit better...so maybe the connectors not snapping together on one of these is the culprit. Or maybe a coil is shorting, or maybe my carbs are a bit plugged, or...I could go on. 

Pretty sure it's a wiring issue so we shall see. I've been daydreaming about rewiring anyway since it's such an ugly mess at this point. 

If everything else is working a by-pass relay might be a cheaper and quicker alternative to diving into a re-wire

wrote:

If everything else is working a by-pass relay might be a cheaper and quicker alternative to diving into a re-wire

Unfortunately, I already have one.

However, I think I found another potential cause - check this out:
 

Really starting to feel the pain of inexperience from when I first started fixing this bike up! At the time I thought that these huge crimp connectors were my only option. Oh well. Slid the plastic back over, heatshrink applied, same situation on the other side.

Also noticed some grooves worn into two of the plug wires...so I rotated them 180 degrees and I should get another 12-15k out of them before that side wears through too.

Fun fun. We'll see if the issue persists once I get out for a ride again. 

In unrelated news, I'm thinking I would like to go back to the 5-speed transmission. No functional issues with the 6-speed, but it feels like I run out of tachometer before I run out of power, and my fuel consumption is not doing awesome. 

Part of that is my inability to stop going full throttle - it's very fun, tiny power wheelies even with my quarter-ton self - but on the freeway I'm running a little higher RPM than stock transmission with a 16" wheel. 

Looks like you have corrosion between the cable and the crimp, if there is enough slack cut the cable back to clean copper and replace the crimp but before you shrink wrap, solder the crimped connector. Once the corrosion takes hold the problem will only get worse as the resistance increases 

Aah, can't believe that I missed that!! Great eye, thank you...