gs500 Engine swap, now no spark

[jesseproctor]

I have a 2004 gs500f that had 30k on it and the counterbalancer was going out (or so I think).  Loud knocking, etc.  Other than that, perfectly working machine.
Found an older engine, late 90s early 00s.  Swapped out the engines.  To keep things simple, I used all of my current electrical, even down to using the '04 cases (carbs, stator, ignition rotor, neutral sensor, etc.)  All connections match, everything is back to normal.
- Engine turns, and sounds great
- All electrical components work
BUT NO SPARK!

Any solutions?? Suggestions??

I tried to heed these tips from adidasguy:
To summarize:

1. Oil cooler: can't put it on an engine that didn't have one.

2. Tach: You can use electronic with older engines if you block off the mechanical tach thingy place on the head. Since your bike is newer electricals, your tach is OK. Plug the hole in the old engine.

3. PAIR system: old one probably doesn't have it. Don't need it anyway. Cap off the hoses and take out that valve thingy.

4. Ignition: Swap the ignition rotor and pickup from the new engine into your older engine.

5. Carb boots: New carbs can fit on old carb boots, not the other way around. Suggest you swap the carb boots to keep the right ones with your newer carb set. Replace o-rings when swapping carb boots.

6. You need to use newer carbs with the newer electricals. Otherwise you also have to change the air box as air intake on carbs is different. Newer bike has TPS and other stuff for electricals and timing.

7. Need to swap the neutral sensor. Newer electricals has sensor for 1st and 2nd for timing adjustments.

8. Engine mounts are the same. Exhaust connects the same. Starter connects the same. Oil pressure sensor connects the same. Spark plugs the same. Voltage regulators the same though stator might have different connenctor.

9. Stator: old engine might have 3 barrel connectors rather than a molex 3 pin connector. If so, you need a connector or you have to remove an adapter that is buried in the 93 wiring harness that goes from 3 barrel connectors to a 3 pin molex type connector on the voltage regulator.

14k miles isn't that much if the engine was taken care of. Why swap motors? Lots of work and I don't see many benefits unless the newer motor is crap.

[adidasguy]

Insure timing rotor and timing pickup are installed correctly and plugged in.
Insure you have a good ground wire connected to the motor.
Re-check all electrical connections.
Engine will not run if in gear and the side stand is down.
Check the handlebar controls KILL switch.
Check wires to coils. They could have been knocked off while swapping engines.

[jesseproctor]

Is there anyway to test the timing rotor and pickups?  There seems to be only one way to install it.  I did notice there is a free floating, small rectangular magnet (approx. 1"x.5").  Where does that go?
Do you have any recommended electrical diagnostics with a multimeter?
Bike is definitely in neutral, handlebar switch is good.  Those would keep it from turning anyway.
I'll look again at the coils.

[adidasguy]

There is no free floating magnet.
Did you take the pickup off of the round donut steel plate?
Did the pickup get broken? (There is a magnet and coil inside of it)
Pictures? So we know what you're seeing and referring to?

[jesseproctor]

Ahah!  The magnet back in the pickup creates great spark!  Duh.  I just didn't know that's where it went.  I do now recall taking off the pickup when I was first looking at it months ago.
Now onto the next challenge...
Bike fired right up.  Sounds awesome.  But, there's a little bit of smoke leaking around the header.  Should I be concerned or should I let heat up and see what happens?  It doesn't seem right, but it could just be getting a little moisture out??
Anything I can do to prevent damage if something is wrong in the top end?
Thanks for your help.  This clearly is my first engine change.

[adidasguy]

Exhaust might be loose.
Spilled oil is always possible.
Run a little to give stuff time to burn off.
If you cleaned the engine, maybe some water trapped somewhere.

[BockinBboy]

Don't know much about swaps other than what I've read on here, so I'll leave that to others... but...

Changing out the engine, I assume oil is transferred/changed/removed/leaks etc  at least once during the process... if it gets anywhere on the headers or pipes you'll see smoke for sure.

A note on the smoke.  Try to determine if its water vapor or oil burning.  Water vapor is white and dissipates pretty quickly and doesn't hand around, though the light exhausty smell does hang sometimes.  Oil burning is usually blue-ish but can appear white in smaller quantities.  It tends to linger for a bit and smells rich. 

Other than that, did you replace the exhaust gaskets?  cost around $5 for two (or cheaper even), and simple to replace.  Only trick is getting the old ones out if they are stuck in there or hiding in the darkness.  They crush together when you tighten them down, and they are meant to be replaced each time you drop the exhaust.  Some folks have taken off the exhaust many times without replacing them and never have issues, while others get an exhaust leak every time they don't replace them 

- Bboy

[jesseproctor]

Well, she still smokes a little, the oil light is on and has a slight knock.
grrrr

[jesseproctor]

If the oil light is on, and disappears when it goes into higher rpms, do I have a bad oil pump?
Is that an easy change? I have a good one on my other engine.

[The Buddha]

If the oil light is on, and disappears when it goes into higher rpms, do I have a bad oil pump?
Is that an easy change? I have a good one on my other engine.

That oil light should be tripped on if pressure drops below @ 3psi.
You may have a bad switch or a bad pump.
Swap the pump first. If it fixes it, I guess swap the switch too. Switch is under the ignition advancer.
Cool.
Buddha.

[adidasguy]

Does the oil light work? Should be on with engine off. Ground the oil light wire if not on and see if it comers on. if it does then bad oil pressure switch.
If light not on when wire grounded, check wiring and the indicator lamp.