Also the last thing " ...place it back in original file you want to play with" confuses me, did you mean I should create the museum in another save file, save to bin, then copy it to my original game?
Yes, I meant that exactly.
As for museum on other lots, not shore where you find it - dynasty museums are always on residential lots. You can't put things from your household inventory on community lots, at least it wasn't possible when Generation came out, not shore after latest patch.
I was able to place things from personal inventory on community lots, including gems and ores.
For some reason game withdraw my Sim belongings once I saved lot to the bin. In your case it returns to your Sim after you leave that lot - you find those gems in inventory, personal or household, or they completely disappear?
Only safe option I know is to place everything you want on empty residential lot your Sim own, move him/her from there and built what you want.
Here is a helpful topic for this issue.After some testing, I find out that I couldn't place photography on walls of comunity lots, not even if I own that lot.
I was able to put cut gem and ore on the ground and they stayed there after I entered Edit Town and put the wall to try to place that photo. You might be able to add gems and relics if you use cheats or purchase property and build from town view->built on lot.
Once I saved file in bin they were returned in household inventory.