ok i just picked up this bike for cheap, i knew it had problems due to being tipped over, i just did not know how bad.

so here are the symptoms:
first initial start up. no choke, starts perfect and runs for 5-10 minutes then it dies.
will not start again for a long period of time such as over night, however it does crank over till the battery dies.
will not start with choke pulled in any situation.

Here is what i did:
checked regulator which was good (i think the leads on the service manual was reversed) as well as the battery.
checked the fuel petcock, and it had a missing vacuum line, however discovered that the petcock was modified, opened the petcock and now verified that it flows fuel. the vacuum line on cylinder 3 is plugged up.
opened the air box and discovered there is pooled fuel on top of the throttle butterfly only in the number 2 carb
the vacuum piston in carb 2 makes liquid squishy sound when pushed (possibly due to the fuel its soaked in)
discovered HRC spark unit intercept , removed HRC and plugged it directly to the spark unit.

next to do.
check spark plugs if good and if getting spark to each unit

what else should i be checking? specially the pooling of fuel, should i be concerned about hydro locking the cylinder?

I don't think one dodgy carb would make it die, it would just run a bit rough/lumpy.

Only thing I can think of right away is a blocked tank-cap vent.
If air can't get into the tank to replace the fuel that's being used, you get a slight vacuum, which can be enough to stop fuel flowing.
Try it with the cap open.

i have the bike sucking on fuel through a bottle
replaced the whole carb set up
checked the spark plugs
replaced the CDI

weak spark though

anything i'm missing?

This is prob gonna sound daft, but is there petrol in the oil? That can make them run strange. Were the carbs you changed them for a known good set? If it wont start on choke there something wrong with the carbs, makes sure the idle screws are all set right.

Morespeedvicar wrote: . . . If it wont start on choke there something wrong with the carbs . . .

Won't argue with that, but it's unusual for it to run fine and then die, if any of the main settings were off, you'd expect it to affect it all the time.

When it's running, does it respond OK to the throttle, i.e. does it rev quickly and cleanly when you 'blip' it?
Do the revs drop off quickly when the throttle's closed again?

First thing I'd check is all the carb settings Don, pilot/idle screws, float heights, balance etc.

Are your plugs black?

its late and im half asleep so this might not be quite right but worth investigating I think based on what ive read.

I think your carbs are running too rich.

This is letting the bike start without choke but when warmed up the engine dies (rich problems get worse as an engine gets hotter)

You want to check that your floats arnt leaking / flooding the carb and engine and your float heights are set properly, and what your pilot srews are set to.

will only be one of those if its running rich, which sounds like it.

on the throttle it responds fine, revs clean and and drops off but it will rev higher for 20-30 secs on the previous set idle speed about 2-3000 RPM higher

plugs are black.

i will check the settings on the carb. any other ideas so while i am at it?

there was petrol in the oil. changed oil cleaned the ground connections on the coil,

the spark is stronger and now it starts and idles at 1500.

however it stutters at 1500 RPM

As has been said, you really need to go over the Carb settings from scratch, including removing the float bowls and giving all the jets and passages a good clean out, and check the diaphragms and pistons while you're in there.
It's unlikely to be anything else really.

going through cammo's tutorial right now.. i got quoted $500 to get all 4 rebuilt and i would rather learn and do it my self