Hello and welcome to the forum. I can't help with the bunks but for the window/water infiltration you might want to look at the bottom of the window molding. There should be a couple of drainage holes. Make sure they aren't clogged with debris. Someone will be able to help you with the bunk issue soon. Have fun and safe travels!!
Rudy, Jenny and Garrett
2014 Four Winds 35SK Super C - Ford F-550, 6.7 Power Stroke- Blue Ox tow bar with Patriot brake - 2004 CR-V, 2013 F-150 and 2016 Wrangler Sahara Toads - TST 507 tpms