SKELETOR
First of all, don't have any buyer's regret over the Freedom 90 var spd model. It is a great furnace. The major difference between the Freedom 90 and the recently introduced Freedom 95 is the secondary heat exchanger which raises the eff rating 2-3% and qualifies for the gov't tax credit. Yes, the AccuClean/CleanEffects can be added assuming you have the space where your furnace is located. What kind of filtration do you have now? Of course this retrofit will be more expensive than if the CleanEffects had been installed at same time as furnace.
Good Luck!