1) Will she just pull down his swimsuit or just pull his manhood out of it to do the matting ?
Since he has no idea the aliens are killers, and is enjoying the encounter with an attractive woman, he will probably remove his own trunks.
2) After mating and they fall asleep the guy pulls his swimsuit fully back on, The alien leader wakes and explores his body while he sleeps. What will she do with his reproductive equipment in the trunks ?
Because lizards don't have such obvious sex organs, she'll probably feel them through the trunks to see if she gets the same response as when he was awake. She may simply hold them and explore them with her human fingers.
3) Would she possible take his genitals in her mouth and explore them that way, what will she think of the taste and the results of his climax?
If she had become familiar enough with human sexual behaviour, she might do this. Being a lizard, this wouldn't be something she would do naturally. She would probably find the taste agreeable. The results of his climax would be similar to lizard results, so she wouldn't find that odd at all.
On to guy B, he might end up being the lucky one being killed outright. He is probably the best for them to use as food as you said plenty of meat on him and a lot packed into his grey shorts.
1) How and where would they grab the grey trunks to remove them?
Probably at the waistband initially, and then they might tug them off by the legs.
2) What will they do with them once they have been removed?
The aliens are highly intelligent and wouldn't do the kinds of things an animal might with the clothing. I suspect they will keep them, wash them, and use them for themselves in their human form.
3) Were might the first alien have grabbed what had been in the shorts to bite it off?
This is one of those things that might be getting too specific for this site, but let's just say at the base, very near the body.
Now guy A That gets experimented on They finish their experiments and use their advanced medical knowledge to heal any wounds he has ,as they don`t want him to die before they can use him . they give him his brief swimsuit back and he puts it back on and they take him to a holding cell .He lays down tired and exhausted ,and soon falls asleep .
One of the higher ranking officers over hears s couple of the guards that prepared and eat the other guys genitals talking about it .He decides he wishes to sample some of this for himself.
He heads to the cell and finds the guy sleeping on his back just in the tight swim trunks .He then starts to run his hands over the guys thighs , and the guy wakes .The alien speaks to him telling him not to worry ,he will not hurt him if he does not resist .
The guy nods and the alien moves his hands up to the front of the tight swimsuit and starts to caress it . As before the guy can`t help what happens and the alien smiles . then sniffs and licks the mass in the swimsuit.
1) Could the alien take the entire mass in the front of the guys tight trunks into its mouth ?
Probably not. The guard has a human-sized mouth and unless he was exceptional, that would be too much for him. But then again, maybe he is exceptional!
2) Would it enjoy the feel of it in its mouth?
Not in a sexual way, but it would probably taste like food, and he would be tempted to eat.
3) What would the alien think of the natural outcome of this activity with the guy.
He would be surprised, but would quickly realize this was a sexual response. He might then be repulsed by the thought of what happened.
4) WOULD THE GUY HAVE ENJOYED THE CLOSE ENCOUNTER?
Yes, since he climaxed. He may have still experienced a little fear, but that can intensify the experience.