Hi Taffed!
Nice to see someone else playing this great FM. Unfortunately you can't complete all the objectives, but what's there is a lot of fun. I'll put each part you need to do in SPOILER so you can try to find stuff yourself first. 
spoiler:First, you need to get into an upside-down room and find a scroll. This is the first objective and isn't too hard to do.
If you can't find it, it's spoiler:on the table on the ceiling. Use a rope arrow.
After that, you only need to stay in the big area you're in now. Follow the pipes around until you can get to the center light (the insectbeast cages will be in front, behind, and to the right of you.spoiler:There's a button on the light stand somewhere. Press it and a cage will open! Use arrows from afar. There's a switch in the cage that will open the next cage, and so on.
Next part...spoiler:OK, let's see if my memory holds up... There's a large base holding the huge thick pillar that holds up the high parapet the archer was patrolling. Get onto the one between the first and second insect beast cages you opened. There will be a small button or lever somewhere on it. This will open a small door on the other large base that sits to the RIGHT of the last insect beast cage. Go there next. There should be a key in there now. From the pipes, shoot a rope arrow up high near a short ladder to the high parapet. You can unlock the blue chest now, I believe. You may have to jump back onto the pipes and take some damage now but you're almost done.
Lastly...spoiler:I can't remember if you have a key for this or need lockpicks, but you just get to the other door by following the pipes to the lowest point. Once you get inside, another objective ticks off and there's nothing left to do. I've tried countless things to get into the area behind the starting point, but no dice.
It's still a fun mission though. Very surreal.