Yes, they stack, but only with curses from different sources and spells.

Notice that the modifiers in the sample effects of bestow curse are untyped modifiers. Untyped modifiers from different sources stack, according to the rules on modifier stacking:

In most cases, modifiers to a given check or roll stack (combine for a cumulative effect) if they come from different sources and have different types (or no type at all), but do not stack if they have the same type or come from the same source (such as the same spell cast twice in succession). — "Modifiers, Stacking", d20SRD.org

So this means that:

• The modifiers of bestow curse will not stack with another casting of bestow curse (assuming you choose the same effect of course).
• The modifiers from casting bestow curse twice and choosing different curses will both work, because they are modifying different things.
• These are equally true for greater bestow curse with another casting of greater bestow curse.
• The effects of bestow curse and greater bestow curse will stack with each other.

Activating a metamagic rod gives you “the ability to use the given feat,” which would then be subject to the rules for the use of metamagic feats—including the one you quote forbidding their use with spells cast out of items. So no, you could not do this. Generally speaking, the only way to cast a metamagic’d spell from an item is to create an item specifically containing that spell already metamagic’d (and paying for the increase in spell level, accordingly).

However, the ring of transcendant spells is worded differently. It does not specify that it allows you to use a metamagic feat—in fact, it doesn’t specify that it’s applying a metamagic effect at all. It just modifies spells you cast, and you do cast spells from wands and scrolls. Thus, it could be applied spells cast from magic items.