So I'm, once again, attempting a play-through of Jagged Alliance, and a thought occurred to me. I noticed that you can pick up items in sector 60. Are these some of the items you see during the prep screen? If so, are you able to leave any items you find in the field here? Seeing as I want to collect as many items as I can in the first few days, I'm going to find that hard to do if I don't have many pockets...

As far as I can tell, the items in the prep screen aren't ones you can find.
That's based upon me leaving Fidel's colt behind and not finding it on day 1.
From memory:
You'll find 1 vest with 4 pockets, perhaps 1 with 3 as well.
You can also find ammo (10 boxes), a gun (S&W), a crowbar, a knife, 1 or more keys, a toolbox and perhaps some more.
If you take 5 ammo boxes per merc, you can equip 2 guys without ammo.
You can also leave someone without a vest.
Knives aren't necessary yet unless you plan to enter the water.

Okay, so my question needs to be altered slightly; is it safe to leave items you find in the buildings in sector 60? Will they carry over to subsequent days, or will they disappear?
My plan for the first few days is to attack a sector, return to base, drop all my loot, 30 GOTO 10 until the end of the day, where I pick up some to go into the pre-day's prep storage. This is so I can get hold of (almost) all the items I find in the field. Something I can't do through conventional means seeing as I'm not currently working with a full squad of mercs.

I've never tried that.
Use a savegame to try.
I managed to take all items I found and needed with me.
You don't need everything you find, especially things like canteens and knives.
As for vests, drop the 2 and 3 pocket ones the moment you find ones with more pockets.
Items like canteens should be stored by 1 merc as you can stack up to 5 in 1 slot.
That saves up carrying space.
Day 1 is the only day you need to spend time in sector 60.
Day 1 I take sectors 49, 50 and 59.
Sometimes with 5 mercs, sometimes with 6, but always including 2 mules (Elio is 1 of them).
As from day 2 1 mule goes full-time repairing stuff.