And to add some more detail...
Some of this came to light when I started my engine for the first time. Engine cranked in neutral no problem, was running for about a half hour. Shut off, turned back on no problem. Ran for about 10 mins this time then it suddenly jerked forward an inch or so. I thought it rocked off the jackstand. Turned it off, started back up and it did it again. Now the car will start but as soon as I depress the clutch in neutral, it stalls out. It's odd it was running fine for awhile before any of these symptoms, did something heat up and break?
And to further clarify, my shift linkage/shifting into gear issue always existed. Both before and after starting the engine for the first time.