Embassy (Malaysia) might ask you to be at best situation(re-apply-print) new passport and then travel. Probably that might not be in your favor. But if it is then this is the best advice.
Could be a problem.. just avoid being at edge(this situation shouldnt be suprise to the officers at airport).Visit Immigration and let them know the situation. Probably they are the best ones to minimise and salvage the most out of this situation