Lol - yes you've got a lot of classic stuff in there! I especially love Kirk charging to the rescue with a ripped shirt. :0
I tried to come at the topic from left field by placing crewmen in peril off the ship for the first story. I thought it would be too easy just to beam an alien off the ship so I tried to think of ways to nip that quick fix in the bud. I love the notion that the aliens are bio-weapons so I linked that into the Vorlon/Shadow conflict. I tried to walk the line between making Rand the damsel in distress and the plucky heroine who can take on the Aliens in her pants.
The biggest problem I've found is that there are just not enough 'action' shots from TMP to illustrate a decent fight. I'd love Kirk to take on a Queen!