What organism are you using? I've attached a paper with good information in the supplement about using long PCR to detect deletions in nematode mtDNA.
The short answer is: buy a good quality enzyme, do a LOT of trouble-shooting, resign yourself to overnight PCR reactions, and keep telling yourself you can't rush quality results. Good luck
Article High Rate of Large Deletions in Caenorhabditis briggsae Mito...