I plan to get the top end of my 525efi rebuilt this winter and plan to pull the engine and send the whole thing to my brother in law in WI to do in his shop. He is going to pressure test the headers and rebuild the top end/check everything over.

Is there anything special I need to look for when pulling the engine that might be a gotcha? I have pulled a couple of car/truck engines in the past. I am going to prep the engine to be pulled and then take it to a buddies shop to use one of his loaders to pull it.

Not really but a couple things.

What size boat/ year? The coupler washer design changed so make sure you keep those (Bell housing to transom plate).
We normally like to check drive alignment before pulling, this will help to let you know if there are other issues.
If its first design CMI's, screw the pressure check, replace them. The pressure check is only good for right then, not fun to find out you have a leak 20 hours in the rebuild.
Good time to clean bilge and changes indicator cables, fix some of Fountains screwed up wiring, put in a oil change kit, etc.

Yes, this!
By checking my alignment prior to pulling motors, I found a rotted center stringer allowing sagging of a motor mount.

2003 29 fountain Single 525 for the boat. I am looking for a set of headers as I have been told this as well.. I am just trying to find a good used set, Cant really afford the 7-8k for a new set.. I wish the stainless marine manifolds didn't require retapping the heads or i would just go with those and be done. Are there any other options here?

You will lose power with stainless marine or the Hardin replacements on a 525.

how much do you pay for skilled labor.........

I make decent old fashionds, but could work something out if you are interested in helping.