Either a dead battery (which I doubt since you said it worked fine on the 4.8) or you got a bad connection or missing ground.

I know when I put my 6.0 in, I couldn't get it started a few times. Like I had a dead battery or something. Turned out that my ground strap that went to the driver side of the block wasn't making a good connection.
How do your cable look? Any corrosion showing on them? Also feel the battery cable wires, if you got a bad connection, the resistance will cause the wires to heat up.

 

check your connections and especially all your ground again. Step 39: http://bertok.us/agreif/engine/EngineSwap.htm

 

just got back from autozone, result: good battery. So it's either a missing ground or a bad starter which is what they thought it sounded like at autozone.

 

It will start, just extremely slowly. Also, it really only starts when it's cold rather than when it's warmed up. I did a search and found a post stating that starters tend to be going bad when they don't start when warm. I already bought the new starter off ebay so we will see if that works. I'll also have the tech check the voltage at the starter.

 

Here's a sound clip I took of the truck starting:

http://www.youtube.com/watch?v=nSAnp5Akn7A

 

Yeah you'll be amazed at how bad a starter sounds when it's not getting it's full power.
I just had a car that sounded just like that. Found it had really corroded positive & negative cables. After replacing them it started awesome.

 

I took off the (+) battery cable and it was very corroded and rusted but everything worked fine with the 4.8. But I think the starts were not as strong on the 4.8 as they had been in the past. Given the fact that the LQ9 is higher compression I don't know if the starter had enough left in it to get the job done. We will find one when I get the new starter put in.

 

I still bet on a bad connection somewhere or possible bad starter (but that would be quite a coincident if it worked fine in the 4.8 before hand).
The starter may not all be the same but I haven't heard of a single person who went from a 4.8/5.3 to a 6.0 and complained about slow starting.

Let us know how the new starter works. Btw, what kind of starter did you get (stock 6.0)?

 

Yeah, I got a new 6.0 starter. It's rated at 1.7kW whereas the 4.8 was 1.5kW. I also do know that before the swap the starts were not as strong as they used to be. Combine that with the higher compression engine and I think that may be the problem. I just fail to see how it could be a bad connection when the starter will turn over when cold but not when hot. The starter should arrive tomorrow but it will be a bitch to install since I have no jack, I'll just have to crawl under there.

 

No factory jack? What would you do if you got a flat?