Planning to switch to a tankless water heater
You cannot combine an exhaust vent for a tankless heater with other vents. For one thing there would be a possibility of the exhaust from the WH going the wrong way in the other vent. The WH must have a dedicated vent.

Also depending on the model the vent may have a requirement for a certain length of vertical run immediately adjacent to the heater before you have a horizontal run. (Tankless WHs with power vents may not have this requirement.)

It will be very costly to retrofit a new vent path for a tankless heater through multiple stories and out the roof. Reconsider your reluctance at venting out a side wall. This would almost certainly be much better, simpler and cheaper. A new roof penetration is an invitation to a roof leak because plumbers in general  don't properly flash a retrofit roof penetration. Ours leaks! 

Even though the current location is not ideal it may be best to use the same location as the current a gas fired tank. Note that the tankless water heater draws a lot more gas when it is on (up to 4 or 5 times more) than a 40 gal or 50 gal gas tank. The gas supply line and the gas meter must be large enough to supply this amount. 

Different models of tankless WH have different sizes and types of vent. It would be a pretty thick wall that would allow one of these vents to be inside a wall.

If the copper water supply piping is in good shape, there would be no reason to replace it with PEX. It may help to put foam insulation around the hot water line wherever you can.

Thirteen years ago we replaced our 40-gal tank with a minimal Bosch tankless WH because twice when our tanks failed they flooded our 1-story house on a slab. If your WH is in the basement, I doubt it is worth it to change to a tankless.

Tankless WHs require periodic descaling with vinegar and they do not supply the flow rate of hot water that most Americans are used to. If you are having a problem with running out of hot water for multiple simultaneous and sequential showering, the best solution is to install low flow shower heads and encourage shorter showers.