Hi Brandon,
Welcome to Marine31Online.com!
If the boat has a lot of oxidation you're going to want a rotary buffer. I use the Flex PE14 with 7.5" wool cutting pads because it's lightweight and quiet. The DeWALT 849X is a great full size rotary buffer but the weight, bulk and noise will wear you out.
I'd recommend reading through these most recent write-up I wrote about how to machine wetsand oxidized gel-coat. Sure you can compound it but it's a lot easer to sand off all the old, dead oxidized gel-coat then to push a rotary buffer into the side of the hull for hours.
How to wetsand, cut and buff a gel-coat boat
As to your other questions....
Rotary Buffer
Yes the Uber Compound and the FG400 will work with a wool pad on a rotary buffer for heavy oxidation.
Flex 3401
You'll have to do some testing with your wool pad on the Flex 3401 to see if it's working for you. These are both great compounds but they are for clearcoat paints and as such the abrasives are nothing like the abrasives used for most marine compounds and polishes with the marine versions being a LOT more aggressive in their ability to cut.
Where the Flex 3401 excels in boat detailing is for boats with only mild to light oxidation. Use the Flex 3401 for this condition boat with a PFW Purple Foamed Wool Pad and a one-step cleaner/wax and you can remove oxidation, polish to a high gloss and leave the surface sealed without instilling holograms like a wool pad on a rotary buffer will do.
