So there's good news and there is bad news.
Good news is, there is a bug in Binary Decompiler tool, which causes cracks on the ground. Bug is not present when using IPL Helper.
Bad news, I'll have to re-do all the work from scratch to properly fix the issue, because, previously edited ipl's by Binary Decompiler will carry on the bug.
EDIT - IPL helper have issues too. For example, take this line
1308, dummy, 512, 2128.25781, 35.17188, 25.64063, 0.00000, -0.00000, -0.00000, 1.00000, -1
IPL Helper turns into this
1308, Item 4, 512, 2128.258, 35.17188, 25.64063, 8.42937E-08, -1.171569E-15, -1.470739E-08, 1, -1
How 0.0000 turns into 8.42937E-08 and what are the effects? Who the f*ck knows.
So, I reached a dead end - There are no current reliable tools or map editors to carry on with this.
That said, I updated the pack again, fixed floating objects pointed out by TWIST_OF_HATE, download link in the OP
Note, there will be cracks on the ground in various places, you'll have to live with them if you want to use this modification.