All of the gains will grow tax free.

We've now, registered our LLC and received our EIN, but looking for assistance with next steps in gaining our first rental property. 

If so, you can exclude 500k.If  not spouses,  unmarried co owner can also exclude 250k each if both meet all the requirements of sec 121.If your gain is not above 250k, only once spouse can meet the requirement and exclude the gain of 250k. 

We get crushed on capital gains in the flipping business. 

Get married and you're exempt up to 500k in capital gains since it's your primary residence (not investment property).

@Jon Lilley have you considered a 1031 exchange to defer capital gains taxes?

Do I just need to pay taxes on the $5K or I have to pay taxes on the whole profit gain?

I'm looking forward to my "new career" and hoping to gain a lot more from Bigger Pockets! 

You probably won't gain much in a refinance because you would probably need at least 20% equity which is about where you are already. 

For now at least, since I have a full time job already and so any gain I make for not doing any work, I’m good with.