i moved your post to the Roo section, under Expandables/Hybrids, since you had posted in the regular travel trailer section and your question is specific to Hybrids.
it would help knowing the model number and seeing pics of the areas of concern. also how long have you owned it?
leaks in the front bunk are usually caused by old/compressed rubber seals, for the age of your Roo.
the above clearance lights could also be letting water get in from bad or old caulking.
a number of people have replaced the wood and door. read thru the Roo section and the Shamrock section for posts about similar issues.
and Zoe the Wonder Dog(R.I.P.)
'07 Roo 23SS pushing an '07 Chevy Avalanche
Equalizer WDH and Prodigy BC