First off.. for the custom PC...
I use an ATI all in wonder type video card.. mines very outdated.. but there are new ones out there that do the same thinglike the ATI radeon all in wonder. provides composite and Svideo in and out, as well as RF in.
My actuall set up here is that I use the RF signal in for all my consoles on a chain, and use the TV tuner feature of the card and software to play my consoles on the computer monitor.
But, I'm assuming you want to run an EMU to your computer..
thats fine.. use this type of card to run your computers composit video output to your Television. badda bing.. I do this for playing first person shooters on the PC on a 32 inch television

as for the joystick mods, there was a gentleman on the forums who was providing this service, but he seems to have fallen on hard times and has pissed off a lot of people.
my person joystick mod played on the gravis mod. but.. I took it a little further.
basicly.. I took an old atari joystick, kept all the guts and did away with the cord..
then, I took a cheap four button gravis game pad.. and chopped up the circut board, so it would fit inside the body of the atari joystick.
basicly.. the only thing left of the gravis pads circut board was the directional button parts and the one button that works with the atari emus.
at this point just solder leads to complete the connections between the corosponding contacts of the two units... seal it all together and now you basicly have a gravis game pad that looks like a atari joystick.. configure on your computer as such.
for two joysticks.. make two joysticks.. then get a game card for the PC that allows the input of two joysticks..
yeah its a little bit of work, and it aint quite the easy answer yer looking for.. but.. it works
hope that helps!