Endogenous

... at whole embryos and the auto-fluorescence was so weak that it wouldn't even be picked up by our most sensitive cameras. I also suspected the endogenous peroxidase activity but that did not seem to factor in either since the anti-DIG + cy3 always worked. I thought of trying cy5 but we do not ...

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yep, it probably will be problem, but if you induce it a lot, you should have excess of your AK over the endogenous one.

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Yeah the endogenous proteins are a big problem. Alternatively I could do a standard maxi-prep plasmid extraction, and use it in a in-vitro transcription/translation system with T7 RNAP then run the blue-sephadex affinity column ...

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you will extract lots of endogenous proteins anyway, because they are present in the cells, although transcription will be inhibited. I would recommend ionex first and then you may try the blue-gel and/or some gel permeation chromatography

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... be expressed. Thus they are expressed constitutively. Thus if the T7 polymerase would be able to transcribe them, it would transcribe also other endogenous genes. But you do not have to worry, since it should be extremely specific . Anyway, you do not use any tag?

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