Shooting these with on camera flash, I should have gone to manual and stepped up the fstop. This would take the variable aperture lens out of the equation and I could have shot consistently.
I think you did very well, other than needing a bit more flash exposure.
The variable max aperture is not a specific problem, other than it increases the probability you were wide open instead of stopped down slightly. Not always an option, but the f/2.8 lens are really good for bounce at f/4 or f/5.
Always watch the Ready indicator for bounce, to be certain it does not flash the insufficient flash power signal. For a hot shoe flash, this shows in the viewfinder too, it is no trouble to see it. We just have to think to look, at least early in the session. You can judge how close to full power you are by the delay until it comes on Ready.
If flashes are remote, you have to look at the flash. The head rotates, so we can place them with the Ready light still in view from the camera position. We can also make it beep. It is good to know though. If it is flashing insufficient power, then increasing flash compensation cannot help, it cannot do more.
I'd get rid of the flash diffuser. Too tiny to help, it just reduces power output. It does allow some direct spill horizontally. It or better a bounce card, can help hot shoe bounce (adds eye catchlights), but a small bounce card can do it better.
Maybe F9 or so? That would have allowed me to shoot higher ISO rightr? Maybe 400 or 800 correct?
There are always more things going on. Stopping down one stop is usually a good thing, but there is probably not enough flash power to shoot bounce at f/9... unless you increase the ISO considerably. Which the ISO would then show the ambient lighting better, but incandescents are orange compared to flash. If intentionally using the incandescents, then we would choose incandescent white balance, and put CTO filters on the flash to make it orange too, to match. If wanting to hide the incandescent orange, then using Manual camera mode allows still setting aperture for flash power (same as A mode), but setting shutter speed high (max sync speed) to hide the ambient orange effect.
I usually use about f/4 ISO 400 for bounce (f/2.8 lens), to minimize the flash power, to insure adequate flash power and faster recycle. On a SB-800, that f/4 ISO 400 will typically (barely) do 12 foot commercial acoustic tile ceilings at full power (hot shoe, standing), and makes lower ceilings be a piece of cake (fast recycle, with lots of margin). If you use camera A mode, you will always have 1/60 second shutter speed (indoors). OK, a couple of exceptions are possible to be slower, but 1/60 does not do anything for flash, but the slow speed can allow hints of the orange incandescents, which some people like the warming. Or camera M mode allows 1/200 second to keep it out, and just use the flash. It is a preference, shutter speed does not affect the flash exposure.