It is quite simple.

1) Pay the owner the amount to settle the loan
2) Then the bank or bike company will cancel the hakmilik
3) Go with the owner to JPJ or UTC or the agent and do the transfer
4) Once transferred, pay the owner the final amount

I am selling my bike and this is the method I tell my prospective buyers. It also has to have an element of trust. Otherwise, do a simple agreement which both parties sign to protect both sides. Or get a 3rd party to hold the amounts and disburse on behalf if you both don't trust each other.

No. I will make sure it is transferred ownership first. He also must have bought his insurance. Anything can happen once he takes the bike away...and it is still under your name, so, a bit dangerouslah for you.