For our rear shocks, the extended length of the shock is actually what limits the travel. I "believe" the Fox shocks are good enough to handle that type of abuse. Alternatively you can use limiting straps to limit your extended length.
I have noticed that the specs on Fox shocks show longer compressed lengths for a given travel than other brands, or I probably would have used them myself.

There are stem converters avaibable commercially if you'd rather just buy them. I assume you must have some reason for not just using a rebuildable stem/eye shock?

As you know, For the front shocks, your compressed length needs to be slightly shorter than the distance between the shock mounts when the Lower control arms are bottomed out, and at least slightly longer when th the upper arms are on the droop stops. (including any adapter/cap you might want to make) It seems that the best way to do that is with an external reservoir shock since the shock bodies can be made shorter when the resevoirs are remotely located.
Too much travel won't be much of an issue for the front shocks, as unused capacity will just keep the shock operating cooler. I really liked the fox shocks too, but you might want to look into another brand that has the specs you need.