Die like in switch killed, die as in slow death, or dies like popping the clutch and stalling it?
If the former, I would suspect a wiring issue like a change in the wires between the years, or a change in the functionality of switches between the years. Suspects, clutch switch, neutral switch, kickstand switch, and for good measures the regular kill switch and the ignition switch. I would start with bypassing the switches to see if the bike still dies.
My bike has the clutch switch issue where you can ONLY start in neutral and you CAN NOT use the clutch.
Being easy-going, (ok, lazy) I am probably not going to mess with it until it fails to start at all...

IF the second, I would look for possible air flow or gas flow issues caused by swapping across the years. Something in the plumbing is not hooked up right etc. Did you swap the carb with the motor, or are you using the old carb?
The third, possible bound-up tranny or something got left out (or in the wrong spot) inside the gearbox.
OH, and did you do the hicky?
Did you do the hokey-pokey? And turn yourself about?
Bleh, mental run-away...
Well, good luck.
Tam
________________________________
From: Patrick
To:
DSN_KLR650@yahoogroups.com
Sent: Monday, October 22, 2012 8:40 PM
Subject: [DSN_KLR650] 2005 KLR Issue.
I recently did an 08 engine swap in a 05 bike. Did the rotor and magneto swap as well. Bike starts up easily and idles fine. The problem is when I pull the clutch in and put it into gear the engine just dies. I have tried to adjust the cable every different way (up at the lever and down on the engine) and it still just dies. Any suggestion as to what I may be doing wrong or what I should be doing differently?
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