IWB chimney repair or replace

I am hoping to get some advice. We have a AHS E140 Wood Gun that is currently hooked up to a masonry chimney. The chimney has two flues side-by-side but only the tall one is in use. The short one was previously used for the oil boiler which we do not use and plan to remove this year. The chimney dates to around 1994 when the whole boiler room complex was added to the building. The part of the chimney above the roof line is deteriorating pretty badly but the part below appears in good shape except for a crack along the mortar line between the two flues and along one of the blocks on the wood boiler side. None of the blocks themselves are cracked below the roofline. I can see three options for what I could do and am not sure what would be best. I could replace the blocks above the roofline on the wood boiler side and tear down the oil chimney to below the roofline and cover it up, provided that the cracks in the mortar joints lower down are not a major concern. I could tear down the concrete chimney to the point where the cracks are and then rebuild the wood side only, or I could tear it down completely and put in a Class A metal chimney for the wood burner. I am also wondering how imminently I should be doing something about the chimney. I don't know how dangerous it is at present. I would really appreciate any advice on how and how quickly to proceed. Thank you very much.
Zach
I have tried to link to the photos of the chimney, I hope it will work.
https://picasaweb.google.com/109808338621160134770/March102016?authuser=0&feat=directlink

Thank you very much. I will do that. Would it be okay to tear down the unused flue to below the roofline and cover over that part of the opening in the roof?

Thank you very much. I have much more experience with roofs than with chimneys, so it won't be a problem to cover the hole. I've been thinking that I should eventually replace that metal anyway, so maybe I will go ahead and do that this year too. I think the smoke must have gotten to it because the other metal roof that was built with the same galvanized panels at about the same time had hardly any rust as of last summer when I was working on it.
Zach