The answer to your question is No, using versatile weapons with two hands does not disqualify them as monk weapons.
But not because of any reason that made you ask the question, because your whole question is wrong as it's clear from your question you haven't understood the paragraph in question.
The paragraph in question on pg. 78, PHB says (emphasis mine):
At 1st level, your practice of martial arts gives you mastery of combat styles that use unarmed strikes and monk weapons, which are shortswords and any simple melee weapons that don't have the two-handed or heavy property.
Let's look at what that paragraph really says.
The first thing it does is stating that at 1st level a monk has a master of different combat styles using unarmed strikes and monk weapons.
The second thing it does is stating that monk weapons are shortswords and any simple melee weapon that doesn't have either the heavy property or the two-handed property.
That's everything that paragraph states. It simply tells you that monks fight unarmed or with monk weapons and then defines monk weapons as either shortswords or any simple melee weapon that isn't heavy or requires two-hands to use.
Simple melee weapon with heavy or two-handed property = not monk weapons.
Simple melee weapon without heavy or two-handed property = monk weapons.
So what about the versatile property? A weapon with that property just gives you the option to use two hands during an attack for greater damage.
However, in this case whether a weapon has the versatile property or not has no impact on the RAW as it only purpose in this case is to define what a monk weapon is, which is a shortsword or any simple melee weapon without either the heavy property or the two-handed property. Any other properties such as light, finesse, reach or versatile has in this case no bearing on the rules. Nor does how you use said weapon.
Yes, your unarmed attack are +4 to hit and deal 1d4 + 2 damage
You can use Dexterity instead of Strength for the attack and damage rolls of your unarmed strikes and monk weapons.
Best Answer
You make your attack with a quarterstaff using Str or Dex. You then deal damage either as per monk level or 1d6 for staff or 1d8 for versatile.
You then choose whether you make a monk bonus action attack or polearm bonus action attack, and get the replacement damage die that comes with the bonus action you chose.
As you gain levels only the monk attack damage would go up; your polearm bonus attack would remain at 1d4. You cannot apply your monk level bonus damage to the polearm bonus attack, but you would gain the bonuses of a magical weapon in that regard, both on attack and damage.
Sidenote: Some DMs may rule that using a quarterstaff in two-handed (versatile) mode doesn't count as a monk weapon, as two-handed weapons cannot be used for monk weapons. Such a ruling would remove the option to make an unarmed strike as a bonus action, but you would retain your polearm bonus strike option. For RAW the option remains.