Let's give 'em separate entries, but follow Demiurge's blueprint.
I'd prefer separate entries too.
It almost looks to me like they got the HD reversed on the bluebottle vs horsefly there.
The Giant Bluebottle has 3 Hit Dice, the Giant Horsefly 6 HD.
That formatting's a bit hard to read, here are the Monstrous Compendium's stats in a bit clearer condition:
Fly, Bluebottle (#AP 1-10 , AC 6, MV 9, fly 30 (D), HD 3, THAC0 19, #Att 1, Dmg/Att 1-8, Morale Unsteady (5-7), XP 65)
Fly, Horsefly (#AP 1-4 , AC 5 , MV 6, Fl 27 (D), HD 6, THAC0 17 , #Att 1, Dmg/Att 2-16, Morale Unsteady (5-7), XP 270)
There's a picture in the Monstrous Compendium of what appears to be a Tasloi riding a giant fly, although it may be another goblin-like creature. A tasloi's 2-3 feet tall and the fly's twice as long as it, which suggests (a) that giant fly is 4-6 feet long, and (B) Small creatures can ride them.
I suggest making the Giant Bluebottle Medium Vermin, and the Giant Horsefly Large Vermin.
As for stats, the Tiny WOTC take on the Giant Fly is:
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Giant Fly
Tiny Vermin
Hit Dice: 1/4 d8 (1)
Initiative: +2
Speed: 15 ft., climb 15 ft., fly 30 ft. (poor)
AC: 14 (+2 size, +2 Dex), touch 14, flat-footed 12
Attacks: Bite +4 melee
Damage: Bite 1d3-5
Face/Reach: 2 1/2 ft. by 2 1/2 ft./0 ft.
Special Qualities: Vermin traits
Saves: Fort +2, Ref +2, Will +0
Abilities: Str 1, Dex 15, Con 10, Int --, Wis 10, Cha 2
Skills: Climb +14, Hide +14, Listen +2, Move Silently +5, Spot +2
Feats: Weapon Finesse (bite) (B)
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Climate/Terrain: Any land and underground
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Organization: Solitary or swarm (8-16)
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Challenge Rating: 1/8
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Treasure: None
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Alignment: Always neutral[/FONT]
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Scaling that up to Medium & Large would produce the following ability scores:[/FONT]
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Medium Fly[/FONT]
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Hit Dice: 1d8+1 (5)[/FONT]
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AC: 12 (+2 Dex), touch 12, flat-footed 10[/FONT]
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Abilities: Str 9, Dex 15, Con 12, Int --, Wis 10, Cha 2
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Attacks: Bite +2 melee (1d6-1)[/FONT]
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Large Fly[/FONT]
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Hit Dice: 2d8+1 (5)[/FONT]
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AC: 12 (+2 Dex), touch 12, flat-footed 10[/FONT]
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Abilities: Str 17, Dex 15, Con 16, Int --, Wis 10, Cha 2
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Attacks: Bite +4 melee (1d8+3)[/FONT]
That looks a bit weaker than the AD&D Giant Fly stats should be.
I think we'd be better off basing the Giant Bluebottle on the SRD Giant Bee's stats, and the Giant Horsefly on the Giant Wasp.
So, how about folding together the SRD Giant Bee & Giant Wasp's Speed and natural armour, the 3 and 6 HD of the AD&D flies and the ability scores given above, but with the bite damage skipped up a step? That would give us the following (modified into 3.5 format):
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Giant Bluebottle
Medium Vermin
Hit Dice: 3d8+3 (16)
Initiative: +2
Speed: 20 ft. (4 squares), climb 20 ft., fly 80 ft. (good)
AC: 14 (+2 Dex, +2 natural), touch 12, flat-footed 12
Attacks: Bite +4 melee (1d8-1)
Face/Reach: 5 ft./5 ft.
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Special Attacks: Disease?
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Special Qualities: Vermin traits, plus more?
[/FONT][FONT=Arial, Helvetica, sans-serif]
Saves: Fort +4, Ref +5, Will +1
Abilities: [/FONT][FONT=Arial, Helvetica, sans-serif]
Str 9, Dex 15, Con 12, Int --, Wis 10, Cha 2[/FONT]
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Skills: ?
Feats: Weapon Finesse (B)
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Climate/Terrain: Any land and underground
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Organization: Solitary or swarm (2-10?)
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Challenge Rating: ?
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Treasure: None
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Alignment: Always neutral
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Giant Horsefly
Large Vermin
Hit Dice: 6d8+18 (45)
Initiative: +2
Speed: 15 ft., climb 15 ft., fly 60 ft. (good)
AC: 15 (-1 size, +2 Dex, +4 natural), touch 11, flat-footed 13
Attacks: Bite +7 melee (2d6+4)
Face/Reach: 10 ft./5 ft.
Special Attacks: Blood drain, disease?
Special Qualities: Vermin traits, plus more?
Saves: Fort +8, Ref +7, Will +2
Abilities: [/FONT][FONT=Arial, Helvetica, sans-serif]
Str 17, Dex 15, Con 16, Int --, Wis 10, Cha 2[/FONT]
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Skills: ?
Feats: --
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Climate/Terrain: Any land and underground
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Organization: Solitary or swarm (2-4?)
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Challenge Rating: ?
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Treasure: None
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Alignment: Always neutral[/FONT]
I think that's a good start.