Is there anything that would prevent me from being able to do that other than chain of title issues? 

I typically buy B or B+ to prevent major rehabs but this is a C- property.

Of course not everything is preventable but at least I did my part in a big transaction.

Repaired water damaged wooden trim along the porch roofline - added drip edge to prevent future water damage.

If you have the money or the access to a loan, no problem.... the money is the on thing that prevents most people from doing this too much.

A wall in the back of the garage showed staining at the bottom and there is that bad watery smell in the basement.

Nathan, if they are the old 1980's/1990s' wood, I have had luck just cleaning/deglossing with TSP (cuts all past oils/dirt from kitchen) and a scrub sponge (use rough side), rinse and then go with Polyshades (stain/poly in one).

What do you do to prevent a great property from being a terrible property?

It it not entirely clear what your question is.Taking a shot in the dark, Unrelated Business Income Tax (UBIT) applies whenever a tax exempt entity (Solo 401k, IRA, or any other type of non-profit) engages in a trade or business on a regular or repeated basis. refer to IRS Publicaton 598.Income derived from passive investments such as rent from real property, interest, dividends and royalties is not subject to such taxation.UBIT was created by congress long before IRA and 401k plans existed, to prevent tax-exempt entities from driving taxpaying businesses out of business.  

See also New Jersey Foreclosure Rescue Fraud Prevention Act