You don't give the total B-vent vertical & lateral lengths and number of ells, which also make a difference. If this is a 2 story with a shallow roof angle, the 4" section could be as short as 8' from where Tee to vent-cap, or it could be as long as 15'. But realistically, best-case, to handle the whole 120K with a 4" stack you'd need something like 30' of vertical 4" stack from the last tie-in, no ells or lateral runs. If the contractor is proposing going with any less stack than that, make them show their math.
Would it simplify the design issues to run a hydronic coil in an air handler running off the HW heater rather than replacing the gas furnace? Even if it meant putting in a bigger-burner HW heater to handle the combined load, something like the condensing 75K Vertex is quite flexible in combi applications, and more than enough water heater for most homes. You have 2 HW heaters here. If an existing HW heaters is reasonably located it might cut the mustard for the heating end, depending on what the actual heat load is. If the new furnace needs to be a heating/cooling HVAC unit there may still be options, but it takes a bit more design. I'm thinking the heat load of a first-floor condo in San Diego can't be anywhere NEAR 45KBTU/hr, (or even 1/3 of that), unless it's a truly huge space with a heluva lot of single-pane glass or something.