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Yes, Mad Doc can join the Kommando unit and come in from reserve at the back of the board. The FAQ states:
"Q: If an Independent Character on a warbike joins Snikrot’s unit before the game starts, can they still turn up using the Ambush special rule? (p62)"
A: Yes.

Also Mad Doc doesn't need to be in the Kommando unit for them to have cybork. As for which model you use as Komanndos - I can't see why not. My only word of caution is to not use them as slugga boyz in the same army list.

Allied Regiments are tough on Orks since they can not battle brother with anyone. But I think any allie regiment will work, you just have to follow the allied rules.

One Scalpal Short has been interpreted several ways.I use it that any unit Mad Doc is attached to can not run, ever and if his unit is within 12" of any enemy unit he must charge.
But some have played it his unit must run towards the closest enemy, if not within 12". Last, he can move or run normally - which can prevent a charge if you see fit. All are within the rules, you should establish which method you are using before the start of the game.

Stikkbombs are Assault Grenades and their use can be found in the rule book under Melee Weapons of the 41st Millennium, subcategory Grenades.