Snow Cat,
Thank you for all this valuable feedback! Some of the issues your experiencing are the same ones others are experiencing as well. I've personally observed while playing the problem with the base pairs being matched but being unable to make any combos with them. It causes the play area to fill up and the player is left not being able to do anything until they pass the bottom border. We're actually implementing some new features and changes in the next two builds that will hopefully fix this issue and the others you've stated. We will definitely let you know when those new builds are published so you may test them out and see what you think about them. Once again, thank you for your much needed feedback!
Fiona Friskee
Head Lab Assistant at Phylolabs