Welcome,

I'm still fairly new myself compared to some of the others who've been around here a while.  I think you'll find it a friendly enough place.

During a flight, if you hit the alt key you have access to a set of menus across the top of the screen.  The Aircraft menu will take you to Failures and "Fuel and Payload".  The World menu will get you to weather where you can change all the things you've mentioned.

Changing fuel and payload can, indeed, change the flight characteristics.  I haven't deliberately tried to put a plane out of balance but I know reducing the weight of the plance can have a big effect on speed, for example.

Now, when you hit Alt the game will pause until you exit the menus and climb back in the cockpit.

By the way, since your question was about a specific version of Flight Simulator it should probably have gone in the FLight Simulator 2004 forum at the top of the Forums page.  People who have your answers will tend to hang out there and you're likely to get a faster response.

And again, welcome.

gw

There's no need to change anything manually in FS9, really.  You can set your weather rate of change high or fly with real weather that updates.

As for failures, if you go into your joystick/keyboard assignments, there are commands you can assign for failures.

Additionally, if you'd rather have a more random but still frequent failure rate for some reason, you can set any system to fail between 0 and 600 minutes.  When it fails is up to you.