1) YOu can reglue the window, but I finally put a new top on. BAS in the UK will deliver a new top to your door fro around $700. Installation is not as hard as you think, many of us replace our own tops.
2) There are drains under the wipers that must be kept clean. Any car sitting under tress a lot get clogged up. THis is an easy fix, the cleanign of the drains, that is.
3) This may be related to 2) but it can also be related to the leaking back window -water can pool in the trunk area and flood the security module, which makes teh lights stay on - the diagnosis that the issue was the light switch/Illumination module is probably in error.
4) If it smoked out the tail pipe, that's a bad head gasket or bad rings - expensive engine work would be needed. If it smoked from under teh hood, it's leaking valve/breather covers - very common and not a hard fix.
5) Big mistake, do not do that again. See my sigline and plug your ears.
6) Many people, some of them my friends, go to eBay for pars. I call these people fools. We can point you to better sources than eBay.

I'd say the first thing to do is to yank the trim from the trunk area and see if the security module is water damaged.