Absolutely. I just didn't bring range into the example, because the situation I described was all in short range.

So a friend and I were playtesting combat to become more than just familiar, as we both plan on Refereeing this game in the near future.

A situation arose where an archer was attempting to fire through two lines of men (allies and enemies) to hit the spellcaster in the rear (who was not engaged in melee). We're no strangers to rulings on the fly so we decided that firing through one line of men would be -2 (partially concealed) and through two lines would be -5 (mostly concealed).

Cool

Then we read Indirect Fire :D It wasn't the part about firing from behind cover that messed us up. It was the part about firing over allies. You need to be a master bowman to use this option and it carries the same -2 as a non-master shooting through a line. We felt this nullified the coolness of Indirect Fire in that moment.

So is Indirect Fire set at -2 because since you're a "master" your penalty is actually a -1, all things considered, or is there something else here that we are missing?

We already have a decent enough house rule on this, but we're not totally happy with it. So I would like to hear your opinions. 

I don't remember much about 3e or 3.5. We didn't play it for very long before we went back to 2e. I do remember it being more crunchy than 2e and that may have necessitated more limitations on stacking? I defer to you on this.

I would be shocked if they didn't stack. Bonuses from stats and class abilities should definitely stack IMO. There are a few class abilities that specify when they don't stack. An example is Berserker's Thick Skin ability which doesn't stack with armor and instead providing a +1. I would say, unless it explicitly states it does not stack, then they do. 

The attack roll modifiers, and ac modifiers from tables 87 and 88 don't stack. Maybe that's what you're thinking of?

If what you listed didn't stack, it would be the first D&D/AD&D that I've played that didn't. Jeff wouldn't do us dirty like that. Let that Zerker rip! Though maybe get some distance first?

I went and got myself confused. 

I'm rolling up a Warlock and was digging into how it would work mechanically.
I found out that they are not inhibited by armor for casting in light and medium armor (the only armor Warlock allows) *Armored Sorcerers p140*

Then I read that to cast a spell, shields should be shouldered, weapons sheathed or dropped. You are also considered 'hindered' -2 AC. *Spell Casting p139*

How would say, a Warlock, with a sword (no shield) and an instantaneous touch attack like Shocking Grasp work? I can't seem to find any exceptions for "fighter/mage" hybrids casting in melee, except for clerics. Would the sword need to first be dropped or sheathed, and then a touch attack made? Would you rule that for such a spell, one hand is sufficient? That round's phases for the touch attack would be spent as Cast/Hold, or Hold/Cast, correct?

Let me know what you think!