Hersh,
I have seen a couple of cars with all pipes running down the centre tunnel & the owners report no real problems except condensation from the A/C pipes.
I am planning to do the same, but have found some wizard insulation for the A/C pipes - high density foam with a "zip lock" joint (like a re-sealable plactic bag) running the length of it. This should sort out the condensation problem (I hope !).
Rather than bring the heater pipes up the tunnel from the water pump, I have welded 13mm stubs onto the front of the S/S radiator pipes (just as they leave the front of the tunnel) at 45 degrees facing forward. In theory, water running forward should branch into the i/c heater pipe & be sucked out the o/g pipe. If the water flow is insufficient, I'll install an in-line booster pump.
After trying all manner of ideas for bracing the pipes in the tunnel, I finally decided that it would be easier to make the tunnel easily removeable - this way I can secure the pipes to the floor at a couple of points down the run & then just slip the tunnel cover over the lot (with a bit of padding).