My father wants to use his SDIRA to provide a loan to the LLC him and I are equal partners in.The loan would provide the additional funds we require to purchase an investment property.The LLC would pay principle and interest at market rate to the SDIRA.Would this be considered a disqualified transaction? 

Yes, you can think of a cost segregation study like accelerating a loan from the IRS. 

Trace AdamsYou hit a lot of good points above and here are some thoughts your should consider:1) IF you’re buying with a second home loan, don’t rent it out long term.

I am doing an FHA loan and will move in once approved.

The Solo 401K would allow a loan, and those funds may be used to invest in your personal name.

I want to see if it's possible to put a new lien on this property so that he can't get a construction loan without paying me back. 

Now assume you buy $350K home; put $25% down and take loan at 6 3/8 on $262,000;  Your payment is $1630/month or you're losing about $600/month all things being equal. 

Lenders would consider modifications in loans or bridge loans, but this is a case by case scenario.

My wife is about to go back to school so she will not be contributing income as well as she will be tacking on a lot more debt to her initial student loans.

You can get “blanket loans” but they’ll be higher interest and make it a little harder to sell.