Much as I hate to inject reality there are a couple of issues here:
Firstly the Glenfarg line diverged immediately after Bridge of Earn so any new line wouldn't serve Newburgh or Abernethy. Equally it probably wouldn't serve Bridge of Earn as the current reopening is proposed for a new development at Oudenard, east of the old station.
Secondly any new line would not have a station at Glenfarg. This would be both because it would need to take a new (tunnelled) route to avoid the M90 and because Glenfarg does not have sudficient population to justify a station.
You also miss out Kelty for some reason, the place on your route with the largest population!
My view is that the only stations would be a new M90 Parkway station somewhere near Kinross services and a new Dunfermline Parkway station around Halbeath where the line crosses the Fife Circle.
Hmm. If Newburgh, Abernethy and BoE/Oudenard were served by new stations between Perth and Ladybank, then which trains would stop at them? Would you have a new Edinburgh-Perth-Dundee stopping service?
In an ideal world:
-New mainline built between Perth and Inverkeithing with stops, as you say, at the M90 at Kinross and Halbeath
-Halbeath station provides interchange with Fife Circle
-Edinburgh-Aberdeen services on ScotRail move (for the most part) to the Kinross route, leaving XC and EC (and some ScotRail) trains running via Leuchars
-Dundee stoppers from Edinburgh are rerouted to St Andrews
-A spur is built off the Fife Circle linking Cowdenbeath to Kelty, where Cowdenbeath terminators now terminate
-ScotRail Edinburgh-Inverness services all run via Kinross
-Oudenard, Newburgh and Abernethy served by EDB-PTH stoppers, which run to a clockface timetable (which is probably impossible, but will be helped by the line through Kirkcaldy losing Inverness and Aberdeen services (though not all of the latter)
Of course, all of this is dependent on the Kinross route being an electrified, high-speed route - otherwise there's no point on moving ABD trains away from Leuchars and the only point of the line is for Inverness trains - which are sped up, and stop at Kinross and Halbeath.
Point 3 is a difficult thing to work out. Do all of the XC services move, or is it half-and-half? There are also other things cluttering this, too - the stations at Edinburgh Gateway, between Ladybank and Perth, and, to a lesser extent, Dundee West/Ninewells (which will essentially replace Invergowrie). Of course Point 1 has to come about before any of this can happen, and I suspect that Point 5 will not happen at all. Cupar and Leuchars also lose services to Dundee and Aberdeen (they definitely need to retain these services at the peaks), and I also think that any kind of clockface timetable between Inverkeithing and Ladybank would prove to be unattainable.
Then, there's one more elephant in the room - Levenmouth. Are there any services that terminate at Kirkcaldy/Markinch that we can extend? Probably not. I guess that new services can run in the place of the INV/ABD services that have moved to the Kinross Line, but those paths will be needed by Perth services. Can they alternate or something?
And there'll be an almighty bottleneck at the Forth Bridge.