2006 Tucson Upshifting

you need to let the RPMs drop down to match the speed you're going for the next gear, though this is less efficient than power shifting through.
Unless you're slipping the clutch to smooth out the gear change, yes, there will be a definite surge every time you grab a gear in a manual transmission vehicle. Most automatics will also shift noticeably harder at WOT.
For more sedate, "normal" driving, you can shift slower and feather the throttle a bit more to smooth out the gear changes, but when you're ******* the throttle as soon as the clutch engages, it's going to be a firm shift. I hope is ok.

Is it repeatable?
Do you notice this when Gears are shifting?
What are the RPMs and/or speed when you notice this?
is the engine cold when you notice this?

Could be a shaft can you smell smoke under the hood if it's the clutch you could smell it burning

Personally, the first place I would be checking is your air filter.

sounds like the torque converter to me maybe a loose flywheel .

check the oil level first ,sounds like low oil level in gearbox

You really should bring this to ford. It could be they have an update for your computer or you may have a torqe converter issue.

You may have a vac. hose miss placed. look at the rear of the manifold for some vac. hoses than may be swapped. Also you may have the throttle\kick down cable out of adjustment or its plastic holder is not pushed all the way into the bracket.

Start with IAC motor, TPS sensor, possible clogged catalytic converter.

From the sounds of it you need to have your transmission rebuilt, there is no quick fix for a fault in one gear. As far as the tapping noise goes quite often a oil change is all that is required to cure it.