Tranny dip stick popping up is not at all unusual but it should not trip a check engine light, mine certainly never does. I suspect dipstick is a bit too long and exerts upward pressure but even if not there is not enough friction between the tube and the dipstick cap to hold it in place. Take a close look at the 2n picture in the 4th post at
viewtopic.php?f=5&t=64217&p=712577#p712577 for a nice solution with a worm clamp and a bit of velcro.
Oil drain plug fix is a Fumoto valve (
viewtopic.php?f=5&t=64217&p=712577#p712577) but if the OEM threads are gone you need to look at geordi's post at
viewtopic.php?f=5&t=63191&p=698855&hilit=fumoto#p698855 to deal with rethreading for an oversize fumoto.
If you have not already done so real Sir Sam's NOOB guide, download copies of both 05 and 06 factory service manuals (05 has illustration keys/06 does not - 06 has diesel cooling section and diagnostics/05 does not) and if you are near or above 100k miles the timing belt replacement needs to be done.