Some of the rules you have might not be what you really wanted. For example rule 27 says that if you place a building at normal ground height next to a raised building the raised building is changed to a raised platform.
Rule 28 says that if you place a raised building next to a platform that isn't raised the platform is raised which is okay if you don't have tiles with raised buildings next to normal height platforms and want to have both on the same level, if however you have tiles of that kind you should remove this rule.
Also placing a raised building next to a forest will change the forest into a raised platform. Is that what you want?
Checking if the rules are causing problems is easy. Just make a backup of the set file and then remove all the rules. They make placing tiles faster, but a tileset can work without them. If you don't have any problems without the rules, there is something wrong with the rules, if you still have the same problem, you have a few wrong tile entries in your set.
Your edge.2da is missing a few entries for raised tiles. If it is possible to have raised platform terrain for example you'll need an entry that says: 8 platform **** platform 1 thf02_z02_01.
Add those lines with height 1 for all the tiles that can appear at a raised height.
You can have walkable terrain below 0. There is no problem with that. Only shadows below 0 will not work properly.