I would say the only way this is possible, assuming the fan (from your picture) is now higher and tilted back from the radiator vertical plane has to be that you didn't re-assemble the crossmember, and/or rear transmission mount properly? Did you replace any of that in the process of R & R of the transmission? It sounds like you had the SBC engine in there with this trans. without this issue *before* you removed the trans for resealing?
That looks like it's tilted back a lot
from the pic, did you replace the trans mount itself with the wrong part (different height, without shim(s))? Could you have put the crossmember in upside down, though not sure it would actually fit to be honest. Did you install the crossmember on the underside of the mounting holes in the frame instead on top? Though again I can't see how you could possibly do that as the bolts shouldn't be long enough to attach it.
I can you tell the 700R4 has two different mount locations; one on the case, and one on tail shaft housing but I don't think that's the case with 2004R? So it begs the question, are you sure you have a 2004R trans and not a 700R4 because if you have a 700R4 and use the wrong mount boss on the trans (on the tail shaft housing vs the case) t will definitely site about 1" lower, and in turn raise the front of the engine. It's easy to tell the two transmissions apart by the trans pan shape (see below). The stock crossmember iirc will fit in different holes (slides forward and back) and line up with either mount point on 700R4.
Here's mine with a G Force crossmember but you can see the tail shaft housing has mount boss (red x), but it's not used, and I'm on the one just behind the pan rail instead.