Welcome to our forum!
I love your critical thinking skills!
I agree that Missler's observations are more or less correct, but his interpretation could be completely wrong, for the reasons you mention. I do believe that aspects of the text show evidence of design, but the ELS are highly problematic. The frequencies of the letters in TORH and YHWH are very high, and so there are thousands of "hits." This makes a careful statistical analysis mandatory before any solid conclusions are drawn.
The best analysis I have read is called Who Wrote the Bible Code by Randall Ingermanson PhD (in Physics). He wrote code to test the hypothesis by measuring the "entropy" of the text. He concluded that there were no meaningful ELS structures in the overall body of Scripture, and I am convinced he is correct. But that would not necessarily imply that there are not some localized patterns, like the ones you asked about. But I doubt they are significant for the statistical reasons you mentioned.
All the best,
PS: I have found some patterns that appear when the text is laid out in a grid, but it is different than the ELS. See The Wheel of Light.