In PA, it's 6-12 months to eject a former owner occupant.

If there is a squatter, you may also need to bring an ejectment or trespass action.

It shouldn’t affect eviction/ejectment at all, this is not a non payment issue, it’s a possession issue

The section on delinquency in rent - repossession by ejectment has the following:"If, in any case of a letting covered by this chapter, whether by writing or parol, the stipulated rent, or any part of the same, be due and in arrear for a period of fifteen (15) days, whether demanded or not, the landlord or reversioner wishing to repossess him or herself of the lands, building or parts of buildings let, or recover possession of the same from the tenant, or any person holding under him or her, shall, without the necessity of notice, institute a trespass and action for possession in the district court where the premises are situated, and in this action the court may award a plaintiff judgment for possession and for all rent due plus costs." 

I'm debating if I should assume a full tear out of the basement bathroom will be necessary - in which case, I'd install a more "belt-and-suspenders" sewage ejection pump (may limit noise generation and risk of sewage back-ups) - and if this is the best path forward, than I'd have to negotiate a pretty substantial price-cut with the Seller.  

The investor estimated that the intentional damage would cost an additional $60,000 to repair and replace.Last year another investor told me he bought a foreclosure house, normally you can't see the inside, and in this case the owner was still living there and had to be ejected. 

Would an ejectment apply in this case? 

You have to eject the prior owner through an ejectment action.

The end is almost in sight - I think the Squatter was finally ejected/evicted November 30th (still don't have confirmation of this), so I will finally be able to close on the property within the next two weeks or so.I noticed that Stony Point, NY real estate lags behind all the surrounding towns and can't understand why. 

Worst case there, if they don't pay you monthly, an ejectment (think foreclosure/court) procedure could be required.In a land-contract, I'd have the escrow agent hold an executed deed from seller to buyer until contract is fulfilled and stay aware that any judgements or liens against seller, subsequent to signing the land-contract, could still attach to the property.This is not legal advice--just lessons learned in the real world.Good luck!