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Regarding plumbing the HX to the water heater: The HX is horizontal and it doesn't matter which line is in or out, but plumb the out to the top of the tank with as little restriction as possible and an up-slope all the way. This will help the thermosyphon affect and, during a power failure, will circulate some water. Assist it with a pump to get the maximum BTUs to your tank. The 007 should be fine for this duty. Use the 3/4" port on the side of the tank near the top, typically, this is the pressure relief port, as the return from the HX.
TEE the output to your floor pump at the same upper side outlet of the tank, where the HX line ties in. Simply screw a brass or galvy tee on a short nipple sticking out of the tank fitting and plumb each line to it. Return the floor loop to the cold inlet on top of the tank. Pull the dip tube out of the cold inlet fitting and set it aside. Put an automatic air vent on the hot outlet. If you insist on an auto fill system, tie it in at the cold tank inlet with another tee.
I suppose the best flow pattern would be to place the HX pump on the bottom line pumping away from the tank toward the HX. Place the floor on the line from the upper side fitting tee, pumping toward the floor. Return it to the cold top fitting as mentioned.
All of this will tend to move air to the tank and get it out of the system. It will not inhibit thermosyphon.
Install tees on the supply and return lines to the floor. One just before the pump, which is pumping toward the manifold. And one after the manifold on the return line to the tank. Connect these with a 3/4 pipe and a ball valve. This will allow you to throttle a bypass and control the supply temperature somewhat. It also reduces restriction in the floor loop. You'll still get all the available energy to the floor, but you'll avoid scalding temperatures and you'll help the pump purge the air. A bit of manual adjusting of this ball valve will get you find the right setting. Probably 1/2 open for starters.
Install a ball valve on the return line to the tank from the floor. Preferably, near the tank. Then tee in a hose bib right before this valve (on the manifold side). You can then close the valve and open the bib to manually purge the floor loops. This will help you get it all started and force out any air.
Again, look carefully at the manifold to make sure you have the loop restrictors fully open. Very important.