This is the number system used by Harley-Davidson circa 1916 into the 1960s.
As a little background info, every year from around 1916 onwards Harley-Davidson made up a special reference model "Layout" sheet. For example the 1925 sheet is titled: "Layout of 1925 Models & Model Numbers." It is very complex and includes: "Sales Dept. Model Nos., Factory Model Nos., Motor Equipped, Motor No., Motor Assem. No. & Frame Number." Later sheets were less complex. Since these were intended for internal use they contain inside info not generally known. Good stuff indeed!
The 1925 Layout Sheet clearly states near the bottom of the page and here I quote: "Note: Motor & Frame numbers start with #1000 and continue consecutively regardless of models...."
It also states this little factoid which I believe refers to the belly/line bore number: "(CRANKCASES NO. 25-1000 & up)."
Clearly by Harley's own Layout sheet engine serial numbers and crankcase numbers in the old days started with #1000 (not 1001).
This numbering method continued throughout the 1920s, 30s, 40s, and into the 1950s. For example the 1938 Layout sheet reads: "motor numbers start with 1000...." and the 1950 sheet reads: "motor numbers start with 1000...."
However, when we reach the 1957 Layout sheet there is an abrupt change in the numbering system. For the 1957 model year it states: "Motor numbers start with 1001..."
No reason for this change was given.
I should point out that both the 1000 start and 1001 start were for normal production models: JD, VL, EL, UL, FLH, XL, etc. Racing engines had different start numbers: i.e. "500," "2001," etc.
In 1960 the serial number system became more complicated swapping starting numbers between 2001 for even (1960) and 1001 odd (1961) years. I do believe that Bruce Palmer mentions this in his restoration book.
In 1970 Harley dropped the old time method and went to the govt. VIN system which has no coolness to it at all.
So you can see this wasn't a trick question, but it has a rather tricky answer. So, if you run across or see a "1000" number don't assume it's FAKE or a Factory only special. It could be authentic normal pre-1957 production.