Upon further review, I'm almost certain Jade Tree has the venue wrong on their videos (maybe even the wrong city, but let's assume they have Philly correct).
Control was released on April 16, 2002, so we have to assume the album was recorded in 2001. These JT videos show that the songs have pretty much the right arrangements and melodies but different lyrics. We know Dave didn't originally intend Control to be a cohesive "concept" album, but he changed the song sequence and some lyrics in the studio when he realized that there was a thread that could connect them all together.
According to the Past Shows
page, these were the Philly shows from that time period:
03/09/1999 Philadelphia, PA TBA
04/08/2000 Philadelphia, PA 4040 (Pedro the Lion with Shipping News, Turing Machine, T.W. Walsh)
09/17/2001 Philadelphia, PA First Unitarian (Pedro the Lion with Seldom, Miighty Flashlight, JV)
We know this video
has the correct venue and date (because it's got the boys from Seldom playing with Dave), so that eliminates the 2001 show from contention.
That leaves us with 1999 and 2000.
So, I'd lean towards calling this a 2000 performance because the songs seem so well-formed, which would put it at 4/8/2000 at 4040 in Philly.
I realize that's not what you originally came here looking for... sorry. Maybe I'll dig into the lyrics a bit later.