On a single engine 25 foot boat with a standard Bravo One drive, what is a good drive hight as mesured from the bottom of the boat up to the cavitation plate?

Use propshaft depth as your measurement. Most will run best at 3-5" below the bottom.

OK. That one is a little tricky to measure. Should it be with the drive trimmed so that the propshaft is parallel to the boat bottom?

Yes. That would put it at neutral trim.

3" is high to me but its a place to start. If you start there you can always shim it down. Its a lot cheaper and more accurate than using shorter drives to get it higher.

I agree, 3" is high.

From your Baja avatar, are you talking a 25 Outlaw???? If so, factory is probably set at about 5" below the bottom. I wouldn't go more than an inch higher than original.
I would also post in the Baja section.

Are you cutting a new transom hole for your Bravo drive, or...?

same reason Im gettin a 2" IMCO shorty installed this winter from Doller Offshore.

No, it is a baja 235 Force. I think the bottom to prop shaft distance is close to 8 inches. Compared to your numbers that must be exceptionally deep. Are there any specific reasons that Baja put it that deep in the first place?
I was thinking of an IMCO shorty as an easier way to do it....
Thanks for your input

I have a baja 24ol my stock height was 7 1/2'' baja's are deep. I went with a 2'' shortie and love it now 5 1/2'' my buddy races a 26sutphen which had a ext box didn't run good so off came the box and then the drive was 4'' it was to high he added 1''spacer now its great, I think smaller than 5'' would work with stepped hulls. when I had the stock height the 3 blades worked better now I use 4 blade trying a 28b1 or 5max this spring through BBLADES program. any help you need let me know. art