1 - if you have GG, Atlas or MTH track (either kind) you do not have to change the trucks as all those track types have essentially prototypically flat or near-flat top rails. "Two-Rail" wheels with the smaller (still not scale) flanges and narrower wheel treads like it just fine.
GG 2-rail O-scale track (yes, they make it) uses the same running rails as 3-rail-O.
2 - switches will be an issue, though. The small flanges and narrow treads will fall into the Hi-Rail flange ways. The 3-axle truck my handle them well, but the leading 2-axle may (will) have a switch tracking issue.
3 - use a portion of your layout with few, if any, switches, for the loco, if possible.
4 - power - tether a 3-rail passenger car "permanently" behind the loco to pass power to the FL9. You can use a rectifier to send DC instead of AC to the loco, if that is what it expects. Is this a straight-DC loco? If not, send it AC from the track by way of the passenger car.
5 - best way: GG track (for example) is set in wood ties, so all the rails are insulated from each other unless you connect them. Don't connect the outside rails, set up a toggle switch or two to choose 2-rail or 3-rail current from the appropriate power sources, and run it as a 2-rail on the 3-rail track. The middle rail just becomes nonexistent, electrically.
You will have to use 2-rail rolling stock with insulated wheel sets, of course.
All of the above takes effort - not to mention your re-trucking idea - and all has been done, here and there. Maybe just wait until the 3-rail comes along?
Or, bash a 3-rail one out of a frame, F-unit bodies and an MTH SD-9 truck. More fun, too.
