I was the first one to recommend a complete switchout of your remotes and distribution system. If it were my job I would not have gotten into this situation, since I wouldn't have put the Harmony's in there in the first place...
However, in my current position where I am working for someone else, instead of for myself, I have the unfortunate experience of using Harmony remotes with the wireless extender. I have found that the 1000 is fairly easy to set up with the wireless extenders (vs. the 890 where I have had multiple problems). Your easiest and cheapest fix, without re-inventing the IR spectrum, would be to put in a Harmony remote extender at each station (8 I believe you said). This would be especially easy since you have already programmed the Harmony 1000's. You would need to put an extender at each place where you have an existing receiver and relay the IR from the exender to your Matrix switcher. I assume you can figure out how to wire this...
This would be the quickest way for you to get paid. Just make sure that you remember the problems you had when you spec the next job so that you don't wind up in a situation where you have to worry about if your design will, or will not, work again. Look into good control solutions that are out there and move away from the things that you can't make money on.
