Well, I haven't messed up that setup on my board if you want to continue playing, but I'd almost rather skip the mess with the first four pieces. I guess if you want to take back your last move, we could go from there with the alternate arrangement of those pieces.
JEDIT: Of course then we'd have two gold generals. I wish I'd played this with someone when I first came up with these rules, but I was all by my lonesome without any shogi partner :'( *sniff*
I honestly think we will need to start over. We haven't gotten too far, and I may want to adjust the other pieces for now as well. And I do need to work tomorrow. What I will do is spend a few more minutes seeing if I like a different setup (probably similar to what you have already done). I will send you my Excel spreadsheet (probably in the morning), either to play with or to rearrange your own. Sorry about the bad news and lack of progress.