Yesterday i removed the cannister, and capped off all the connections it had used.

Now i want to change my fuel filter, and i see that the current one has three ports.

I'd expect two ports -- fuel in and fuel out.

So what is the third port for, and does it go back to the tank or what?

I want simple.... fuel comes up, and into the carb.

Can i replace it with a simple 2-port filter and cap off whatever the third connection is?

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'87 D150 Slant-6 A904 with wooden cap

Why? Disabling the canister is not only unsafe if done wrong (which it sounds like you might've), but even if done "right", it's not an upgrade, it's a downgrade.
Discussed in Fuel line mod.
You sure you wouldn't rather have the setup that works best, instead of the setup that is "simplest"?

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一期一会
Too many people who were born on third base actually believe they've hit a triple.