>So every chance i get I am fixing that and pressing them together to leave space at either end to allow easier frame removal. I think that will make a really big difference.
If you start out that way it's best. Trying to convert is more difficult as they are often too fat to fit well. Be careful you don't have comb against comb this way.
>Lastly, something simple I had missed - when I was scraping burr comb
There's one of your problems.
Try leaving it.
>or trying to put a cover back on that had huge amounts of bees clustered in the way, I used to just blunder through, usually upsetting/killing a lot of bees. On the weekend I consciously used a lot of smoke until they all got out of the way. Once again, no squashed bees. In some instances this took a heap of smoke (note that I wasn't blowing it into the hive, just across the top to move the bees out of the way).
Sometimes a brush is more useful. But be sure to flick them out of the way and do NOT gently brush them ever.