D&D 3.5 equivalent of PF 1.0 Persistent Spell Metamagic

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.

No.

While the text of the feat is somewhat ambiguous, there are several indications in the rules that touch spells are not valid targets of Persistent Spell:

• If spells with "a fixed range" were intended to include touch spells, why are spells with Personal range called out as allowed? After all, "Range: Personal" is no more variable than "Range: Touch."
• The errata for the book in which Persistent Spell was originally printed, Player's Guide to Faerun, explicitly said that touch spells could not be persisted. While subsequent re-publishings of the spell did not include these changes, they're indicative of what the intent of the feat's wording was.
• Heroes of Battle p. 113 describes the effect of War Weaver's Enlarge Tapestry class feature:

Spells you cast through an eldritch tapestry have their range category increased: touch spells become close range, close-range spells become medium range, and medium-range spells become long range. Long-range spells and spells with fixed ranges are unaffected.

This rule explicitly draws a distinction between touch spells and spells with fixed ranges, and treats them differently, implying that touch spells are not included in the category of spells with fixed ranges.