Personally, I'd just look at either replacing the heat exchangers, or the whole unit (might be cheaper depending on how much tear-down is required and how hard it is.) Pinholes means corrosion, and I'll bet there's a lot of very thin metal now.
Dad used to have a combination wood/oil furnace in the old house. We discovered that we just had to plan on replacing the heat exchanger in it every 3-5 years as it just corroded out.