Daid,
Have you guys looked into using Vespel as a material for the insulator, instead of PTFE? It's what Stratasys uses as an inlet for their FDM heads. It's got excellent insulating properties.
Also, some of the issues you're having might be mitigated by software. What if you automatically cooled one head down before printing with the other one? It wouldn't need to cool down completely, just be at a "standby" temperature, until it needs to be used. This would slow things down when doing dual extrusion prints, but for certain use cases, it would be just fine (for example, printing support).
Since no manufacturer has perfect dual-extrusion working, even this kind of interim solution would be much better than nothing I think.
Rim