I don’t think you can

Chain Spell says a spell that specifies a single target, and chain lightning specifies more than a single target. They don’t seem to work together.

The most reasonable interpretation, assuming you wanted it to work, is just to have two separate chains: the chain lightning one, and the Chain Spell one. Strictly speaking, though both specify that no target can be struck more than once, those are separate rules so someone hit by the original chain could also be hit by the Chain Spell chain, except for the first target. That doesn’t seem altogether unreasonable to me, balance-wise, but it does seem counter to the probable intent. Actually, combining them at all is probably counter to the intent and the actual wording.

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.