CPU doesn't fit

No good, starting with this details (although I could not fond motherboard with suffix with O - just X9SRL-F)
Motherboard link
Single Socket R (LGA 2011)
    Intel® Xeon® processor E5-2600/1600
        and E5-2600/1600 v2 family† (Sockets FCLGA2011)
        (up to 12 cores and up to 130W)
CPU link
TDP  140 W
Sockets FCLGA2011-3

Looks like the MOBO accepts E5-1650 v2 where the v3 is apparently a different socket?

Yes.
And even if it fits TDP don't match!!!!
TDP must match

as far as I can tell, those should be fully compatible.  So, 2 options:  either one of the parts isn't what you ordered, or possibly there's some orientation problem.

Close visual inspection of both parts should confirm their actual models:
click on image to enlarge:
http://www.itcreations.com/view_product.asp?product_id=37182

how is it not fitting?

Doh!  That seems to be the issue.  Thanks for the input.

searching here for e5-1650 shows both v2 and v3 variants with the same socket:
http://www.cpu-world.com/cgi-bin/SearchManufName.pl?MANUF=&NAME=e5-1650&FLAG=&PROCESS=Search&TYPE=CPU&SEARCH_TYPE=1
 - 2011-land Flip-Chip Land Grid Array

So, it should physically fit.  I don't know if TDP would be an issue, as the Thermal Design Power is to do with heat generated, and we don't know what cooling rig is being fitted (or its expected usage)

Hi Dan, the CPU has four notches (two on each end).  The notches don't quite line up to the socket.  If I get the notches to line up to the posts, the corners of the CPU go past the corners of the socket.   If I get the corners to line up, the notches are too far from the posts to let the CPU drop down to the pins.

I have another question:

https://www.experts-exchange.com/questions/28548882/Mobo-and-chassis-backplate-how-to-cable.html

can you guys help with this?

https://www.experts-exchange.com/questions/28553081/Server-build-CPU-fan-speed-problem.html