Did he do the furnace install into a pre-existing duct setup? That's what it sounds like. If so, he really isn't responsible for the pre-existing condition. It sounds like your house was not built very well in the first place for HVAC, since it lacked proper insulation and ductwork. By your brief description regarding only ceiling ducts, etc. I would guess that he is right and that your duct work is inadequate. The furnace doesn't matter if the ductwork isn't done right. Sounds like his plan may be the right way to go. These are fairly complicated issues and it is hard to be 100% sure with your relatively brief descriptions. My guess is that he is on the right track.
Why did you replace your furnace? If you thought that alone would fix your problem then it might be possible that he could have just done these duct and zone improvements and you would have been alright. If your furnace was old and clunky then it maybe DID really need replacing and he was just hoping that it would fix your problem. If your house is relatively small and not spread out into wings then you might be able to get away with just adjusting the individual duct dampers in the basement to better balance the system - but you might actually need a zoned system with powered dampers and multiple thermostats as he proposes. Adjusting at the floor or ceiling vents doesn't work very well so don't try it. It sounds like you might have inadequate returns and that may be what he is also addressing. The attempt to boost the fan speed doesn't sound like a good idea. Typically, you try to keep the fan speed as low as possible when heating in order to keep the heat transfer efficiency high, maintain high temp air to the supply side of the system and to reduce any drafty feeling. Faster air is good for A/C but not for heat. I would get a detailed estimate from him and also from at least two other reputable area contractors and seek their input as to what they think might fix the situation. It is much cheaper if you can get away with just new ductwork and not the zoning, but not always possible.