quick question

[rmkrider]

i recently blew the crankshaft in my 98 rmk 600. wrather then spend the money to buy a new one i picked up a used motor for a couple hundred buck. i wanted to ride when i went home for xmas so i had the guy i bought the motor from drop it in for me (he is a very smart mechanic). when the motor was first put in it ran great... when i got the sled it ran like crap. when u fire it up it sounds like it runs on one cylinder. sprk is good. reeds are brand new and after i cleaned the carbs it ran good again. after sitting for a week or so i went to start it and it did the same thing as before. any suggestions as to what the problem is... my guess is some sort of wiring

p.s. it will fire and run, on one cylinder, but if it stalls it doesnt want to start again