My 2006 BF225 also surges at low rpm and stalls or fall back to idle sometimes when trying to get on plane. I think it was the fuel issues and I think I fixed it as I tried 5 times in the last couple month it ran smooth, no beeps, no surge, no stalls...etc. Hope I fixed the issues as I can't get to the VST tank to clean it.
What I did was removed the anti siphon valve that's on the top of the fuel tank, you can replace with new one if you want, but for me, I drilled the hole bigger to get the valve out (small ball and spring inside the connector).
But before that, I did many work to it.
Replaced sparkplugs, all the fuel filters, water separator filter, only use Non-Ethanol fuel (as ethanol fuel leave water in tank), thermostats, water temp sensors, cleaned throttle, replaced gear oil, impeller (clean and lubricate the shaft too).