Best Of

follow the manual,

except, that air intake, looks weird, I would expect you want the 12 inches from the bottom of the intake gooseneck, to the roof deck directly below the intake, not to bottom of rafters at the deck penetration,

call them and ask to explain why the intake is on the deck

Do what is in the installation manual. That is the best advise. If there are several options, then select the one that you are the most comfortable with. But don't just make something up that is not in the manual because of some other piece of equipment used that design. Only use those options that are listed by the manufacturer. If for some reason you have an existing vent from an old appliance that you wish to re-use, then take a picture of that exhaust/inlet vent system and see if you can get the Tech Support people at the manufacturer to approve it. Email is the best way to do this, because you can print their reply and keep it with your I/O manual for future reference.

That 12 inch minimum to the rafters on a sloping roof might work — if you never see snow and the roof is flat or nearly so. Otherwise it's just insane.

What @hot_rod said. Panel rads; abandon the in floor system. Can the boiler be salvaged with repiping?

A floor build up over an existing slab can mess with anything already in place, door opening heights, cabinets, plumbing rough in, headroom, and worse case any stairs between levels would need to be rebuilt so all the rise is, I think, + or - 3/8 of and inch, by code around here.

Even 3/8" variance between treads turn into a "tripper" which you can feel, especially in the dark :)

A radiant ceiling gets you that same quiet, comfortable radiant feel, and may be easier to retrofit. It usually costs you an 1", tube, furring strips and new sheetrock.