could a mis-installed lower intake cause coolant in the oil/cylinders?

It's possible. I'll see if I can dig up some vac schematics for you.

yes if the lower isnt sealed good it can leak coolant into the oil and into the cyclinders via intake runnners.

Here are some pics I saved from another thread

i actually ran the lines a different way. i capped off the one that's closet to the t/b where coolant used to run through on the old egr plate and plugged up that line. then i went to the parts store and picked up like 1' 1/2" of hose line and ran that from the charcoal can(s) to the back of the intake where it goes to the vaccum tree on the firewall. then i used the elbow to connect the hose to the vaccum on the firewall. then i connected the PCV to the "nozzle" right under the tree and everything else was connected regularly. much easier to route, JMO. car runs just fine