The original pony express you reference did not have a paper stamp but used handstamps at both San Fransisco CA and St Joseph MO. The initial rate was $5.00 per 1/2oz. I think this is all you will find on the surviving covers carried during the 18 months it existed.
Where I run into trouble is that you also find these Wells Fargo stamps on covers carried by the pioneer pony express riders. You also see some regular issue stamps where they entered the mail at the St. Joseph terminus.
Richard Frajola has an amazing database on these rare and very valuable covers. Each east and westbound ride is numbered chronologically an so are the surviving covers.
As to the Wells, Fargo and Co. stamps, they began as agents for the Central Overland, California and Pikes Peak Express Co. in April 1861. The first 2 stamps were #143L1 ($2 red) and #143L2 ($4 green) until July 1861 when rates were cut and the #143L3-143l5 were issued.
This reduced rate is where my stamp fits.

Also during this period Wells Fargo won a government contract for it's mail service, so from July 1 to Oct. 24 1861 stamps issued were considered official use.
Hope this helps a bit James, I'm still learning myself.