I gave up on constraining my image output in PS and started exporting blocks without defining project bounds. I find it MUCH easier.
I have been getting good orthophoto results using gdal to make a .vrt (using gdalbuildvrt) from those blocks, then pulling out my AOI using gdal_translate to create tiled tiffs from the .vrt. You can make a bigtiff (>4GB) if you really want to by tweaking gdal settings (actually I think it does it by default if it calculates a >4GB tiff filesize). If I weren't sharing the imagery with others I'd probably leave it as a .vrt and build tiles that way.
My parameters (optimized for filesize, quality, and rapid display in ArcGIS, and I left the filenames in because I think they're mostly explanatory):
gdalbuildvrt -srcnodata 0 -vrtnodata 0 Elwha_20140812_merged.vrt 20140812_Elwha_RGBAvg_WGS84*.tif
gdal_translate -of Gtiff -co "COMPRESS=JPEG" -co "JPEG_QUALITY=90" -co "TILED=YES" -co "PHOTOMETRIC=YCBCR" -co BLOCKYSIZE=256 -co BLOCKXSIZE=256 -co "TFW=YES" -projwin -123.6118356 48.0112936 -123.5745359 47.9572204 -b 1 -b 2 -b 3 Elwha_20140812_merged.vrt Mills_20140812_RGBAvg_WGS84.tif