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I've been working on a semi-basket case 2003 R6 off and on since February. Race bike, crashed, was put away wet and then a young racer snagged it to revive but ran into two small problems: 1) No mechanical training and 2) No budget due to breaking his shoulder blade and thus no lawn mowing. So I got it. Some of the stuff was pretty easy to sort back out, front brakes self locking due to a dirty, dirty master cylinder that was plugged up, etc.
Where I'm flailing is with the motor. When it arrived it would start, with heavy coaxing from the throttle. It would run rough, throttle response was delayed, as in seconds, kinda creepy. Hit the throttle and it'd bog, close it and a second later it'd build revs all of a sudden. Whacky crap. Tank had either diesel in it, or the worst aged out gas I've ever seen. Yanking the PC3 eliminated the odd throttle lag. Leak down test showed one cylinder clearly had multiple valves hanging open, borescope showed serious carbon / crap buildup in all four. Pressure plus a hammer cleaned the crap off the valves, swapped the two shims that needed tweaking after, rebuilt the fuel pump, cleaned the throttle bodies, injectors were all professionally cleaned and balanced, plumbing and wiring cleaned up, new airfilter to replace the decaying 'thing' in the airbox...
Still doesn't run right. It fires up cold, idles beautifully. It'll snap to on small throttle movement. If you give it a full twist at low RPM (6k and below) it'll bog / stumble / misfire and not build revs. Ease it up around 8k with light throttle, whack it and you get full song of it's people. I've no place to road test, so this is all on the stand, in neutral or 6th for max 'load' doesn't matter. It's running SO much better than when it arrived, but clearly something is still out of whack. It's got a slip on exhaust, I don't think it's a full system, I've added slide stops, other than that it's stock. I have a PC3 which I've updated to current, it was literally on the first shipping revision, I had to get a rev box to update it... I have the Graves sample slide stops 03 R6 map loaded, it expects a full exhaust and I think a different air filter, but the bike behaves the same with or without the PC3 connected. The map really doesn't tweak much.
It might just be in desperate need of a remap, but I can't imagine it running so badly off the stock ECU with as few mods as it has. This has me hesitant to toss it on a dyno just yet only to find out that mapping isn't going to cure it. I suppose it could be a 640 monster motor in disguise... but I'm not holding my breath on that one just yet.
What's the hive mind got for suggestions on what to check next?
leakdown - good
compression - good
valves - adjusted, timing as per service manual
new plugs and coils
new OEM air filter
injectors Pro-Flowed
throttle bodies sync'd at both idle (bleed screws) and 1/3rd throttle (butterflies)
fuel pump rebuilt
Supply side fuel line replaced
TPS and other sensors appear to be good based on diag mode readouts
Cleaning, so much cleaning of everything...
And yes, the ground is solid.