If by standard, you mean manual transmission, here's an example picture of a shifter and linkage.
I don't mean to sound crass but honestly speaking, if you are having trouble just separating the shifter from the transmission, your success rate of removing the engine and transmission without damaging anything is not good... much less working on either and re-installing both properly.
That being said, there's only one way to learn
and to answer your question:
When I did mine... In a nutshell, I removed the three linkages to separate the shifter from the transmission.
I marked each linkage to identify and note length, then I took pictures.
I then disconnected the shifter from the linkages at the shifter side, labled "linkage g clip" above.
I then disconnected the 3x linkages from their respective levers because I figured I'd bend them if they were there.
Good luck and most importantly, have fun & welcome to SV!