Ignition + fuelling control unit dead.

I have been without my Bike for almost 2 months now.
What seemed to be an idleing problem is now a dead control unit (computer). I purchased a new one on Ebay.. and the mechanic managed to get it to start once and then it wouldn't start again. So now my concern is that if that indeed was a working unit... then my bike shorted it out... if it was no good then I should just buy a brand new one. I'm getting desperate and and I'm about order a brand new Unit online for many $$$ and im worried about plugging it in if there is a chance that it can get fried.

Is there anyway to test these units without having to plug them into the bike? and is there a way to find out if something else is the problem. Mechanic said he tested all the wires/breakers and seems fine. Is he missing something, is there any other units that precede the connection into the computer unit. (i dot know anyone else with a 2004 sv60, contacted one person selling one online but no reply)

Has anyone had a problem like this before? what was the resolve?
(FYI this is my first bike and excuse my terminology)

thanks In advance.

i miss my baby

[Sid Squid]

Is there a fault code listed whilst the 'dealer mode' is engaged? If yes, which code?
It is possible that an electrical fault could damage the control unit, but it would need to a be fundamental problem and thus should be obvious and easy to diagnose. You need a properly specified manual that lists fully the test criteria for all the ancillary electrical and electronic parts, they must be fully tested before going any further.

thanks for you advice Sid,
This a better history of what I going on:

So this is what happened/ing: I started having Idling problems on my bike late last year probably around September time.
I didn't know what to make of it at first, it seemed to be associated with going up in altitude. So i thought it was something to do with mixture control or something like that. Although i took it up the mountain a bunch of times and it was fine... So it was inconstant. I took it to a shop for service and they said they couldn't replicate it.. so They just increased my idle speed and put a band aid on it and. That didn't help at all. It kept happening intermittently and most often after riding on the highway when i would slow down the bike wasn't able to idle. I would be able to keep some throttle in and be able to make it home and the next day it would run fine again (well idling when warming up sometimes it would be slightly erratic sometimes).

Eventually I took it in for my next 14,500 mile service to a different shop and told them about the problem. They also said that they couldn't replicate it .. but said that my throttle bodies where out of sync and that should do the trick. I picked the bike up and was supposed to head back to work since i left early but right as I got off the high way and put the clutch in at the light is stalled instantly. This time it was having even harder time idling. it was seemed worse then when i brought it it! So i drove home worried that I would be able to start it again. And surely It wouldn't start the next morning. I managed to get it to turn over once and then once the next day, since the shop that worked on it wasn't returning my calls.. for a few days... and I had to wait till the weekend for them to pick it up since i work they seemed really reluctant to do it. I just wanted to get my Bike working again.

Here is what the came up with [this is a copy of their report]
"the unit was inspected and the following was noted:"
"-Confirmed no start on Unit, the spark plugs were inspected and found to be fouled (cleaned) [probably from me trying to get the bike to start,
that or they didn't do the job the first time],
-fuel pressure was inspected and found to be good (45psi),
-compression (1/0 frnt and rear) [i think thats what it says print is cropped],
a leakdown test confirmed only a 2% leakdown through the cylinders (good),
-the stator cover was removed and the engine trimming was inspected and found to be good,
-a fuel flow amount test was then performed and the unit is flowing at a rate of 165ml per min (good)"
"Suzuki was then called and all numbers where confirmed.
The only test still available would be to swap out the ECM with a known Good ECM from a2003 to 2007 sv650
the unit requires a new magneto stator cover basket" [what is this? just noticed this note]

they didn't charge me for this service since it was on 30 day warranty from their last service that killed my bike... grrrrrr.
So I don't know if they are at fault of what.. I retrieved my bike and told them that I couldn't afford to replace the part at this time , mainly because they wanted to mark me up at least $200 on top of $650-800 it would cost for a new CDI [from wast i was able to find online]. Also When i called to tell them that i was coming to pick up the bike, they told me it was ready for pick up. With a friend and his truck on our lunch hour we came to the shop.. and teh bike wasn't ready parts where open and he spent at least 20 mins rushing to get it ready.. So I got the bike on teh truck and he handed me a baggy with a pin from the gasket in it. Saying oh make sure you put this in the bike before you start it. WTF!! I didn't say anything just wanted to get out of there and deliver it to a new mechanic so he could assess what is missing etc.

Now the bike is at my neighbors shop I purchased a used CDI on ebay and he plugged it in He got it to start and it ran. But heared som clunking so he stopped it and found that there was another pin missing. SO he replaced it and then later in the day when wanting to test ride it he couldn't get it to start up again. He said that he maybe heard pop and think that maybe the cdi fried.. (?) i cam e to pick yup teh bike he told me that he couldn't get it to start again. and they are not able to get spark.
Since then he said that they tested all the wire and they seem fine. So mayeb teh CDI was no good since it was used and off of ebay..? or something else is wrong and possibly maybe the bike shorted out the cdi (if that is possible)

Not sure what to do next. Is there other things that should be diagnosed that could have been overlooked.

any help advice is really appreciated.
Thanks again.

[Sid Squid]

FI bikes, (like yours), have barometric sensors for both atmospheric and airbox pressures thus, (within reason), raised altitude shouldn't cause poor running. Throttle balance can seriously affect the bike's idling, but unless the bike is otherwise running correctly adjusting the balance is meaningless - it's the job you do last after ensuring all else is well as other adjustments will affect it.
The report: They say the stator cover was removed to check 'trimming', I take it this means timing, did they remove the cover or just the inspection plugs? There's no need to remove the cover to check ignition timing and indeed of you do, you can't check it as the alignment marks are on the removed case! Anyway, as the ignition system has no moving parts and the electronics are very solid and relaible, if there are sparks at all it is usually safe to consider the timing correct - at least initially anyway. I suspect the engine's left front side case was removed as the part referred to as 'stator basket' almost certainly means 'stator gasket', the only reason to replace this would be removal of the case.
Mechanically the tests done suggest the engine's condition is good - the compression figures are, as you say, truncated on the print-out, but the leak down test does not give reason to consider anything is amiss.
I am concerned about the bike being started with a part, (pin?), missing, what is it that was not fitted? And where from? Is it possible that the engine has suffered some damage by being run with a piece missing from the mechanics of the engine? What was the 'clunk'? Check this first before going any further.
Do you have access to an electrical meter, and are you able to use it? Agfter making cerain of the mechanics I'd continue by obtaining a wiring diagram and checking all the relevant cabling for continuity and the connectors for security and condition, and then ensuring the various parts that should be fed with voltage are suitably fed. A 'pop' suggests an electrical failure - but from here it's impossible to know what!
I also suggest not taking the bike back the original garage - the service seems poor to say the least, it is possible that you will need to find another with a better commitment to customer service - no disrespect to your neighbour but you need to find somebody able and familiar with these sort of machines.