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Converting Links:
When changing links to replacement knuckles the cars become very far
apart when coupled.  So much so that I converted my AF heavyweights back
to links.

Flyer compatible:
The AF compatible couplers made by SHS, AM & Downs all seem to work well
with Flyer. My favorites now are the newest AM couplers that allow close
coupling between cars, essentially a scale-like look.  These are
available separately.  Older AM couplers snagged on AF switches.  Newer
design seems OK.  The SHS also work very well with each other and AF,
but in mixing all the varieties I find that the squarish shape of the
SHS causes some problems behind an AM geep with body mounted couplers.
SHS are fine other truck mounted AF type couplers or with any loco with
truck mounted couplers.

Mixing Link and Knuckle:
I prefer to handle link and knuckle by having a couple cars with both.
An ideal solution I've used is to mount a link and knuckle on opposite
ends of the same truck. Spin the truck 180 deg, and presto, you have a
car that lets you handle everything.  Amazing what you can do with epoxy!

Kadees:
I also run Kadees on superliners and AM heavyweights and they work
well.  I made mounts so they are truck mounted.  The Amtrak loco has
body mounted Kadees and this forces some restrictions like no flyer
radius ess curves allowed.  I have not converted freight cars to body
mounted Kadees yet because I am not sure I want to deal with these
restrictions.  Especially when the close mounted AM couplers give
roughly prototypical car spacing.