Issues with ordiplot3d NMDS in 3dvegan package - vegan

Question

I am looking for some help here with this 3d NMDS code. I have 3 issues.
The layout of the plot moves significantly each time I execute the code.
The sites and species are sometimes far off of the plot.
The species text is often overlapping. How can I fix this?
I am unsure how to change the plotting environment to ggplot, so that might be out of the question.
library(vegan)
library(vegan3d)
library(tidyverse)
data("dune")
SiteID <- 1:20
NMDS = metaMDS(dune,distance="bray", try=500, wascores = TRUE, k=3)
NMDS1 = NMDS$points[,1]
NMDS2 = NMDS$points[,2]
NMDS3 = NMDS$points[,3]
NMDS = data.frame(NMDS1 = NMDS1, NMDS2 = NMDS2, NMDS3 = NMDS3, SiteID=SiteID)
NMDS_input <- metaMDS(dune,distance="bray",try=500,k=3,wascores = T)
pl4 <- with(NMDS, ordiplot3d(NMDS_input, pch=16, angle=50, main="Fish ion level 3", cex.lab=1.7,cex.symbols=1.5, tick.marks=FALSE))
sp <- scores(NMDS_input, choices=1:3, display="species", scaling="symmetric")
si <- scores(NMDS_input, choices=1:3, display="sites", scaling="symmetric")
text(pl4$xyz.convert(sp), rownames(sp), cex=0.7, xpd=TRUE)
sii <- as.data.frame(cbind(NMDS$SiteID,si))
with(NMDS, orditorp(pl4, labels = sii$V1, air=1, cex = 1))

Answer 1

labels must be character variables in orditorp. We always assumed so, but this was not checked in vegan::orditorp. Latest vegan version in github will take care of this and will also work with numeric labels.
ordiplot3d returns projected coordinates (in 2D) and if you want to plot those, you can just use the pl4 object that you saved and you do not need to use pl4$xyz.convert. This object will also be accepted in orditorp.
If you want to plot points that were not used in the original mock-3D plot, you must use pl4$xyz.convert for their 2D projection. This function will return the projected coordinates in a form that is directly accepted by standard R functions text, points (and some others), but they will not be accepted by orditorp (and I won't change this). You must make these into two-column matrix-like object; data.frame() will work.
Your example code contains a lot of un-needed code. The following is an edit with only necessary lines and fixes that make this example work with current vegan release.
library(vegan)
library(vegan3d)
data(dune)
SiteID <- as.character(1:20) # must be character
NMDS_input <- metaMDS(dune,distance="bray",try=500,k=3,wascores = T)
pl4 <- ordiplot3d(NMDS_input, pch=16, angle=50, main="Fish ion level 3", cex.lab=1.7,cex.symbols=1.5, tick.marks=FALSE) # no with(NMDS,...)
sp <- scores(NMDS_input, choices=1:3, display="species") # no arg scaling in scores.metaMDS
text(pl4$xyz.convert(sp), rownames(sp), cex=0.7, xpd=TRUE)
orditorp(pl4, labels = SiteID, air=1, cex = 1) # character labels w/points in the same location