Heres my rules for Alpharius based upon Legion that i posted on the B&C:

Alpharius Omegon

Ws Bs S T W I A Ld Sv
Alpharius 6 5 5 5 3 6 4 10 2+
Omegon 5 6 5 5 3 6 3 10 2+/4+

Pts: 450

Wargear (Both): Power Sword, Silenced Bolter, Frag and Krak Grenades

Silenced Bolter: When firing with this bolter and the sentries rules are in play the shots are not detected by the sentries.

Special rules:

Master reflexes: Alpharius had incredibly well developed reflexes and could dodge bullets. This benefits from a 4+ invulnerable save. If Alpharius has not joined a unit any weapons firing at him that are not Template or Blast must re roll any Passed to hit rolls. This rule only affects Alpharius.

Heads of the Hydra: Alpharius and Omegon are the only twin primarchs. As such they are often in battle together. If one died the other would take his place, personifying the hydra. As such the must be fielded in the same army but may be placed in different units.

Master Tactician: Alpharius Omegon was a master tactician and was always in control. As such at the start of the battle the player may nominate two stealth units. One of these stealth units must be lead by Omegon. The stealth units must always be kept in reserve, even in missions that do not use the reserves special rule. When these units become available, the owning player rolls a D6 to determine where they deploy from:

1-3: Own players table edge
4: Left short table edge
5: Right short table edge
6: Opposing players table edge

Sounds good. Small point, what codex is this to be based off? (what would the stealth squads be?).

Did you introduce the variation in attacks and ballistic skill for just variance or for fluff?

Do they count as a separate HQ each, or are they bought as one entry?

They are 1 HQ entry. The variance was for fluff and to make them a bit similar. The stealth squads are any unit nomiated.

So a Terminator Squad with Land Raider transport? :D

Ah yea that might be a problem. I think ill need to restrict it, any suggestions?

I would say restrict it to a normal tactical squad/CSM squad, but give them further options to take silenced bolters and other cool wargear... Maybe a couple of sniper rifles?

I think im going to have to make a seperate entry for them. So watch this space...