I think you will need to drop the trans and pull the top cover to reinstall this stuff. Been 5 years since I had a T5 apart. You may want to get one of the online diagrams or overhaul postings and see exactly how this is assembled.
Oh man that sucks. On the newer transmission there is a label that says, "do not remove" or something like that. I agree with rd, i believe you'll need to take it apart(atleast the lid).
Next time remove the shifter and *slowly* pour the fluid down the shifter hole. This is the easiest way to fill a trans. It helps if you have another person to watch the fill hole underneath to start dripping a little fluid so you know it's full.
I fill my T5 by using an appropriately sized clear plastic tube, inserting one into the tranny and routing the other up into the engine bay, where an assistant pours the fluid into a funnel into the tube, and I stay under the car to make sure all is well.
I could do it on my own, 'cause the tube sticks in far enough to hold in place, and I just keep funneling the fluid in until it's near capacity, and then I watch for it to come back out of the fill hole, indicating that the unit it full.
I can relate to the poster's error - I had a brand new 1993 Chev Cavalier with a manual trans, and the first time I went to change the fluid I ended up removing the completely wrong "bolt" which looked like a good candidate for a drain plug to me at the time. I got lucky - bolt went back in and my dad is still driving that same car with the original tranny in it today with almost 150,000 miles on it. I was 19 and "winging it". I'll never do that again.