Welccome aboard from a fellow 9600 owner! 
Impressive looking setup you have... mine is a fairly meaty setup also, but definitely not quite in the league of what you describe above. I'd definitely say a 9600 constitutes vintage by this point in it's life, and at that, what a machine they are!
Mine is an early revision (non-Kansas) 9600/200MP... I bought it because it was the dual-604 200MP model and I always wanted one, but seeing as though I also had the option of buying a Crescendo G3 upgrade I used that as it makes it far more useful and versatile for the best part. Spec's are as follows...
Sonnet Crescendo G3/400-1M @400MHz with 1Mb cache
512Mb RAM (there is a heap more waiting to go in when I can be bothered rearranging it to maintain interleaving.)
10Gb Ultrawide SCSI main HDD
7Gb and 1.5Gb secondary HDD's.
8x CD-R burner (no rewrite capability)
TwinTurbo128 8Mb full-length PCI graphics card... this is a stock Kansas card. The pre-Kansas 9600 had a TT128 4Mb.
Ultrawide/LVD SCSI PCI controller
10/100 PCI LAN card
4-port USB PCI card
Dual-USB/dual-Firewire combo PCI card... this is likely going to be removed and replaced with the 3-port Radius MotoDV.
Targa2000 capture/display out output card.
Software-wise, it runs OS9.2 via OS9-helper, and also has XPostFacto and an OSX installation, however I don't really use it as my experiences with OSX on oldworld Powermacs have been fairly lame.... I experimented for fun on the 7600 years ago and whilst it was a cool little development, OSX is simply too slow. 10.2 and prior were slow even on supported hardware, and in this current age, anything priuor to 10.4 is next to useless, with there being better software support for OS9 and 8.6 by a great margin. I have a full complement of professional software such as Premiere, Photoshop, Illustrator, SonicWorx, FlashMX, Fireworks, Freehand, to name a few.... I'll be re-exploring the functionality of some of these when I acquire some period peripherals such as an ADB tablet and a functioning analogue video camera.
It is basically used as my go-to machine for anything I cannot do in OSX or with modern hardware, which is a lot... basically it's my vintage support workhorse, and I also have intentions to start using it for some of what it was designed for. I used the 7600 for analogue AV capture and manipulation years ago, but I want to take it up to the next level with some real horsepower now that I have it available.
Some points worthy of note are that It did have an R7000 64Mb that for some unknown reason I have been anable to get to display video on this machine... It also will not display video on one of my two 16Mb Rage128 cards (both OEM Apple items), however all of these cards work in my G4 Sawtooth, G4 Yikes and Yosemite G3... havent tried them in the 7600 or the beige G3 minitower as yet. I know as much as other people have reported similar issues with x600 series towers.
The Targa2000 card (A very very high-end full-length, dual-board capture and output card that also supports full-resolution and depth svga output, dual-display output as mirrored or spanned) will ONLY work correctly when placed in the 2nd PCI slot from the bottom... it failed to work properly (or at all in some cases) in other slots, and also caused conflicts with other devices as well. I found out later that the vendor actually specify that it MUST be placed in this slot to work properly. I wonder if this may also be applicable to your card and account for at least some of the niggling issues you are having also?
Impressive looking setup you have... mine is a fairly meaty setup also, but definitely not quite in the league of what you describe above. I'd definitely say a 9600 constitutes vintage by this point in it's life, and at that, what a machine they are! Mine is an early revision (non-Kansas) 9600/200MP... I bought it because it was the dual-604 200MP model and I always wanted one, but seeing as though I also had the option of buying a Crescendo G3 upgrade I used that as it makes it far more useful and versatile for the best part. Spec's are as follows...
Sonnet Crescendo G3/400-1M @400MHz with 1Mb cache
512Mb RAM (there is a heap more waiting to go in when I can be bothered rearranging it to maintain interleaving.)
10Gb Ultrawide SCSI main HDD
7Gb and 1.5Gb secondary HDD's.
8x CD-R burner (no rewrite capability)
TwinTurbo128 8Mb full-length PCI graphics card... this is a stock Kansas card. The pre-Kansas 9600 had a TT128 4Mb.
Ultrawide/LVD SCSI PCI controller
10/100 PCI LAN card
4-port USB PCI card
Dual-USB/dual-Firewire combo PCI card... this is likely going to be removed and replaced with the 3-port Radius MotoDV.
Targa2000 capture/display out output card.
Software-wise, it runs OS9.2 via OS9-helper, and also has XPostFacto and an OSX installation, however I don't really use it as my experiences with OSX on oldworld Powermacs have been fairly lame.... I experimented for fun on the 7600 years ago and whilst it was a cool little development, OSX is simply too slow. 10.2 and prior were slow even on supported hardware, and in this current age, anything priuor to 10.4 is next to useless, with there being better software support for OS9 and 8.6 by a great margin. I have a full complement of professional software such as Premiere, Photoshop, Illustrator, SonicWorx, FlashMX, Fireworks, Freehand, to name a few.... I'll be re-exploring the functionality of some of these when I acquire some period peripherals such as an ADB tablet and a functioning analogue video camera.
It is basically used as my go-to machine for anything I cannot do in OSX or with modern hardware, which is a lot... basically it's my vintage support workhorse, and I also have intentions to start using it for some of what it was designed for. I used the 7600 for analogue AV capture and manipulation years ago, but I want to take it up to the next level with some real horsepower now that I have it available.
Some points worthy of note are that It did have an R7000 64Mb that for some unknown reason I have been anable to get to display video on this machine... It also will not display video on one of my two 16Mb Rage128 cards (both OEM Apple items), however all of these cards work in my G4 Sawtooth, G4 Yikes and Yosemite G3... havent tried them in the 7600 or the beige G3 minitower as yet. I know as much as other people have reported similar issues with x600 series towers.
The Targa2000 card (A very very high-end full-length, dual-board capture and output card that also supports full-resolution and depth svga output, dual-display output as mirrored or spanned) will ONLY work correctly when placed in the 2nd PCI slot from the bottom... it failed to work properly (or at all in some cases) in other slots, and also caused conflicts with other devices as well. I found out later that the vendor actually specify that it MUST be placed in this slot to work properly. I wonder if this may also be applicable to your card and account for at least some of the niggling issues you are having also?