Tom, all the original hoses should be there. I didn't remove anything when I installed the level 2 kit. Only the hose from the IC bango bolt to the cycling valve was cut with one end going to the MBC and the other end being sealed up with a bolt and jubilee clip (you can see in the photo). The car was 100% and completely stock and unfettled with before I got my greasy mits on her!
I didn't bother removing the cycling valve because I wanted the mods to be reversible, but what Thom (TTM) says is right - you may as well ditch it.
Another job you might consider is the deletion of the vapour purge system. This involves the removal of all the associated hoses and components including the charcole cylinder in the offside wing and fitting a fuel tank breather. For some reason Porsche produced cars between certain years without a vapour purge system at all so it appears to serve a function that can be done without. It is quite a common mod in the states. The benefits are reduction of clutter in the engine bay and removal of boost leak opportunities.
Looking good Tom, looks like you are lavishing alot of TLC on her. Is that a nice new water pump gasket I can see? what have you done so far? timing belt, rollers, tension and water pump?