Multiple Metamagic Feats, Spell Slot Adjustments and Effective Spell Level

Question

In our current 3.5 module, my brother plays a Sorcerer. His favourite antic is Ray of Enfeeblement. He always casts it as a Chain and as a 9th level spell to do inflict a 9d6 strength penalty. I believe in the mix he's also using Empower Spell and Heighten Spell.

My question: When multiple metamagic feats alter the spell slot, and Heighten Spell is used in the mix, does the final spell slot determine the Heighten Spell effect, or only the levels adjusted from Heighten Spell?

Example:
Ray of Enfeeblement (1st level spell)
+ Chain Spell (+3)
+ Empower Spell (+2)
+ Heighten Spell (+3)
= 9th level spell

Thus, in this mix Heighten Spell only increases the spell slot by +3 in total (Basically a 4th level spell slot), however the final spell fills a 9th level slot.

For determining the benefits of Heighten Spell, which "effective level" would the spell be cast at?

Ray of Enfeeblement

The subject takes a penalty to Strength equal to 1d6+1 per two caster levels (maximum 1d6+5).

Chain Spell

Any spell that specifies a single target and has a range greater than touch can be chained so as to affect that primary target normally, then arc to a number of secondary targets equal to your caster level (maximum 20). Each arc affects one secondary target chosen by you, all of which must be within 30 feet of the primary target, and none of which can be affected more than once. You can choose to affect fewer secondary targets than the maximum.
A chained spell uses up a spell slot three levels higher than the spell's actual level.

Empower Spell

All variable, numeric effects of an empowered spell are increased by one-half.
An empowered spell uses up a spell slot two levels higher than the spell's actual level.

Heighten Spell

A heightened spell has a higher spell level than normal (up to a maximum of 9th level). Unlike other metamagic feats, Heighten Spell actually increases the effective level of the spell that it modifies. All effects dependent on spell level (such as saving throw DCs and ability to penetrate a lesser globe of invulnerability) are calculated according to the heightened level.
The heightened spell is as difficult to prepare and cast as a spell of its effective level.

Answer 1

You would cast a 4th-level Ray of Enfeeblement, and it would cost a 9th-level spell slot.

Without Heighten Spell, it would be a 1st-level Ray of Enfeeblement costing a 6th-level spell slot.

Metamagic does not increase the effective level of a spell. Instead, for powering up the spell with other effects (like chain and empowerment), you pay the price of a higher-level spell slot for a lower-level spell. If you wind up with a 1st-level spell taking up a 6th-level spell slot thanks to metamagic, it's still a 1st-level spell.

Powering up the effective level of a spell is exclusively the role of Heighten Spell. Think about it: if Chain Spell meant you were also casting an effective-level-4 Ray of Enfeeblement, what would be the point of Heighten Spell even existing?

See the bolded text here, in which it increase the effective level of a spell - emphatically, unlike other metamagic feats:

Heighten Spell [Metamagic]

Benefit: A heightened spell has a higher spell level than normal (up to a maximum of 9th level). Unlike other metamagic feats, Heighten Spell actually increases the effective level of the spell that it modifies. All effects dependent on spell level (such as saving throw DCs and ability to penetrate a lesser globe of invulnerability) are calculated according to the heightened level. The heightened spell is as difficult to prepare and cast as a spell of its effective level.