I think it just takes patience and care to get the batting back together smoothly. I am in the process of putting together an almost-queen size Log Cabin that I quilted in 7 different sections. I did not want to wrangle the entire top even if the batting was divided, so I broke the top into those 7 sections and quilted each one, leaving the last round of logs unquilted. I'm using the same method you are (the fusible tape) to join the batting except that I have two layers of batting (what was I thinking?) and pinned the top rather than using the spray basting. I have a little bit of rippling but the final quilting should take care of that.
I struggled to get the first two sections together but the next two went together MUCH easier. So maybe your second joining will go easier for you too. Perhaps the length of the join is the issue...seems that a longer length would be harder to manage.
Hang in there!
AnitaSt