Exactly, CYL 1 is set to TDC on the compression stroke; then the cams are set to TDC with a camshaft alignment tool (ford part# T94P-6256-CH). Put the belt on; set belt tension.
There is no adjustment able to happen in the stock system (except in 9 degree increments). So maybe one of your cams is off by a whole tooth Paul. You might want to look into that. It would cause a serious loss in power.