What a great story! And I can't think of a better start in the world than that wonderful exhortation from such a great man, and a true statesman. I'm sure your father could not help but live a "happy, active and useful life" after that!
I highly recommend you write the story down, if you haven't already done so, and keep a copy with the letter and handkerchief so that whomever you pass it on to knows it and will appreciate it as much as you do. It will also help its value.
As for value, looking at recent comparables in the sales records, an embroidered FDR handkerchief of this sort is, as far as I know, unique or extremely rare and on its own would sell at auction for more than the autograph, that is, in the range of $500 - $800 and so has a 'replacement' or insurance value of at least $1600.
The signed letter is worth in the range of $400 - $600 at auction. 'Replacement' value $1200, for insurance purposes.
So putting the two together, and including added value for this unique story, they would have a 'replacement' or insurance value of at least $3000.
As far as safe storage goes, the items need to be in archival storage bags such as this:
in a separate bag for each item. This is a special kind of archival grade plastic that is acid free and chemical free to protect the paper and keep it moisture proof. Remove the letter from the envelope and store each one separately between two backing cards, also of archival grade. Don't stick them to the backing card, though, as the adhesives may harm the paper.
Your local Hobby Lobby or art supply store usually carry these archival items.
If not, they are readily available on line from a number of sources:
Keep them away from direct sunlight as the UV rays can make the paper and cotton fabric brittle.
That's all you need to do other than consider keeping them in a metal or fire-proof safe.
I do hope this helps!
Please let me know if you would like further assistance with this, I would be glad to.