Edit: Trying to make this less wordy without dropping relevant content.
In Star Wars Insider #87, the article Order 66: Destroy All Jedi features an in-universe report for Palpatine by presumably Sate Prestage. It states the official number of Jedi survivors at less than 100, or approximately 1% of the Jedi Order (unofficially, sources used in How many Jedi were there at the time of the purge? puts the final survivor count is at 200+, but the percentage isn't tied to this number).
That puts the Jedi Order at 9-10,000 strong. I assume the in-universe derivation of this percentage is based on some census obtained prior to the Clone Wars, during the Order's last known steady state.
To exterminate the Jedi order, Palpatine needs to kill 10,000 Jedi. This was achieved by:
- Being KIA during the Clone Wars (No. of in-publication deaths: 303)
- Being scattered across the galaxy commanding the GAR for easy pickings when Order 66 came down (430 Jedi officers, 1 each commanding 10 System Armies => 20 Sector Armies => 80 Corps => 320 Legions)
- Anyone in the Jedi Temple during Operation Knightfall were massacred by Darth Vader and the 501st Legion
Before leaving to confront Palpatine, Mace Windu had the Jedi Temple fortified, armed and on alert to an imminent Sith attack. Lightsabers were given to every last Jedi, even younglings. Although Palpatine had the element of surprise - Darth Vader and the 501st Legion were not initially recognized as the enemy - this didn't last long as Vader announced his intentions immediately upon entering the main hall (the first room and before the clones started fanning out). It was enough however to force the Jedi to start evacuating the younglings and Padawans, though most of them didn't escape successfully.
During the Clone Wars, when Captain Rex led the 501st and 212th to arrest Jedi General Pong Krell, the Jedi Master demonstrated the capability to hold off with his 4 blades 11 clone troopers when surrounded on 3-4 sides (The Clone Wars, Season 4 Episode 10) - and that may not even be the most he can handle.
A Jedi Knight on alert can reasonably expect to hold off with 1 blade 3-5 clones surrounded. Masters can maybe handle 7-9, but these guys are mostly dealt with by Vader, not the clones. This suggests that the 501st Legion, numbering 9,216 at full strength, could handle an alerted Jedi garrison of an estimated 1-1.3k, less to further guarantee success.
Order 66 was issued at 2100 hours and ended before daybreak. Assuming Vader had an average kill rate of 1 Jedi per 5, 15 or 60 seconds for 9 hours, he would be able to kill up to 6.5, 2.25 or 0.5 thousand Jedi that night respectively. The expected casualties in the Jedi Temple during Order 66 can be estimated to 1.5-7.8k Jedi if the massacre lasted all the way to daybreak.
From the above figures alone, 2.2-8.5k Jedi are accounted for - a lot of which heavily depends on how fast Vader kills Jedi - 4-4.3k dead Jedi is a more likely figure (at 15 seconds kill-rate). These are all uppermost estimates.
The way I see it, the remaining Jedi have to be either on missions separate from the war (likeliest to survive), be attached to the GAR in non-officer roles or be part of the unofficial existing casualties of war. Depending on what you believe about Vader, that can be over one or eight thousand Jedi to be accounted for in this manner. Are there any evidence to support this as the likeliest case or any evidence to correct any of the math thus far?