Ryan,
Thanks for the help. On that diagram the lower cover, the middle bolt hole on the left is covered by the oil dipstick tube. If you look at the diagram (hard to see) there is semi-circular channel in the ribs between the top and middle bolt hole that the tube runs up through/against The clip (item number 3) clips the tube to the lower cover to hold it in place. Mine is a late D16Y7 (SOHC no VTEC) motor which might be different from other D series. I think other D or B series motors have a bolt to hold the tube in place.
Turns out from reading on Honda-Tech that the tube is held in place on my engine by an o-ring. You just have to pull hard to pop it out. I managed to get it all back together and running last night. I didn't drive it to work today as I still need to finish filling up the coolant. I let it run last night, but got tired of waiting for the thermostat to open up so I could top the coolant off as well as burp it to get any trapped air out of the system. I also haven't reved it higher than idle, so I need to test drive it. It did start up just fine.
By the way, were did you get that diagram from? The version of that diagram that is on the Majestic Honda parts page is crappy. It seems like I used to have a link to some other online parts place that had better images than Majestic (you could even click the image if I remember correctly to link to parts), but the prices were not as good as Majestic.
That diagram was worth much more than my Haynes manual.

It had instructions for how to deal with the balancing shaft belt and other stuff that is just not on my engine. Basically the instructions sucked.
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Richard Casto
1972 Porsche 914
2013 Honda Fit Sport
2015 Honda Fit EX
http://motorsport.zyyz.comMoney can't buy happiness, but somehow it's more comfortable to cry in a Porsche than a Kia.