Kevin ~
I am no whistle mechanic, so take this for what it's worth.
I do restore a lot of weird mechanical things, especially auto-related mechanics. When someone brings you an irreplaceable engine from a 1906 Golden Arrow and wants what appears to be a slime covered stone broken down and rebuilt, you have to get creative sometimes in getting things apart that have been married 100 years!
Your pipe wrench predecessor sounds about typical for anyone setting pipe in a day when steam fitting and locomotives were as common as dirt, ... just spin it on and wrench it tight.
Heat will break the worst rusted together parts I have ever encountered. Head bolts snapped-off flush, with easy-outs snapped off in them! Get the bolt red hot and allow to cool and it will often come out with little effort. I use max heat as a last resort and am aware of sometimes needing to re-temper certain metal parts. Patience and soaking would always be a better choice, but then when wouldn't patience be a good idea?
I do not know if railroad mechanics treated steam fittings like plumbers treat chrome fixtures today by wrapping them in cloth or leather to grab, but not bite the surface, or if they just torqued something like a whistle with a bare wrench (?), but I suspect they did the latter, making wrench marks par for the course and historically accurate (?)
I DO know that we all like stuff to look nice, but sometimes we need to temper our expectations to match the historical "patina" of years of service and maintenance as what it "should" look like.
We have enough people hanging around this joint that good advice should be in no short supply.
Good luck!