I told him that I just replaced the roof with brand new roof, not sure how that "bring" down the neighborhood.

Eventually you do have to replace big ticket items like roofs and appliances.

Also, ideally my goal would be to take a row house like this in my neighborhood, raise all the floors and roof so that all floors including the basement have at least 9'-0" ceilings, and turn the building into three units.

Chimney penetrations in the roof are future leaks.

And check that they did not omit anything from the reserve study (whether it be roads, parking areas, roof, pool, fencing, detention basins, etc); you will probably have to go through the entire property covered by the HOA to see whether they covered everything.

Would you just include the HOA dues in that 50% since they take care of roofs, maintenance beyond the walls, etc?

Also, at this time I do not know the condition of the roof, hvac, or any other major components.

However, setting aside money for maintenance each month is more geared towards not only common repairs that could come up every month, but saving for bigger repairs down the road (roof, HVAC, etc).

The HOA received a settlement against the builder's insurance for $1 million and decided to spend it on fixing up the building: replacing roof, re-painting, addressing cracks in the stucco, etc.

If the roof or furnace need fixing, or there's a tax bill due, those bills have to be paid by you and your IRA, proportional to ownership percentages.