Help with oversized furnace causing short cycle
There is no reason that you should have that much variation in your basement and top floor.  It is either a storage area or a living space.  If it is a living space then you have a huge insulation issue down there.  Trying to solve that via more registers is idiotic.  If your main level is heated properly a well insulated basement should need very very little heat.  Any living space should have access to heat/air but the last HVAC guy sold you his stuff without fixing the problem.
Do not restrict the airflow.  If you have to constantly close registers or are adding filters this is a huge waste of money.  You are burning fuel to have a good percentage of your air hit a dead end.  So this just makes no sense at all.  
Understand that your main HVAC issue is the size of the unit.  Anything you do to cripple the output will cost you money and your unit will not last as long.


Options...


Insulate your basement.


2a. Sell your furnace, install properly sized one.

2b. Live with what you have.  Let it do its thing.  Keep thermostat upstairs.  Understand it will short cycle when it is warmer out.  

The problem is most HVAC companies you call will know you have a problem and will solve it based on what they are best at or what makes them the most money.  And unless you allow them to tear the whole thing out none will fully guarantee a marked improvement.  And of them giving advice about filters or doing whatever to make your system less efficient I would never do business with them.