It's the clutch pushrod, #1 here in the first diagram.
When in place it is seated within the bore in the in the diaphragm spring #3 in second diagram. Like kaopano said, once you've pulled back the transmission back a couple inches, you should be able to get your fingers in there and pull the pushrod back so it retracts into the transmission where it will reside while you remove the transmission from the bell housing. If it didn't come out of the clutchpack and is stuck, it's possible that the clutch diaphram spring shifted somehow during the installation of the clutchpack and is now pinching the pushrod so it won't slide out easily. If the spring is not centered properly and is pinching the pushrod, it might affect the balance of the clutchpack and result excess vibration on rotation. At any rate, I think if you remove the six bolts that hold the clutchpack together, the whole thing will pop off and the pushrod will become unpinched and will likewise fall out. Be careful not to bend it if it's not already bent.
If like kaopano mentioned you put any pressure on it while removing the transmission, the pushrod may be bent. You mentioned that the ABS got in the way because you had to pull the transmission all the way back off the still-seated pushrod. I don't know how you'd get the transmission off anyway with the ABS units still on. When I pull the transmission, I've always had to remove everything that might obstruct the transmission on removal, that includes both ABS modulators, which can be tied up to the frame with bungees other such methods along with the footpeg plates and calipers without disconnecting the brake lines. You have to remove the battery tray mount, which also includes the mounting arms for the ABS modulators, to get the transmission out, so the ABS units have to come off those mounts anyway, no?
Anyway, on reassembly, the pushrod lives in the transmission. When you put the transmission back on, you line up with pushrod end with the hole into which it gets seated, and push the transmission on that way. Don't suffer needlessly -- read this before reassembling.
http://www.motobrick.com/index.php/topic,7086.msg48744.html#msg48744