I drilled a tank for the first time about two years ago and kick myself for not doing this on my previous setups; the process is unbelievably easy. I know you mentioned not wanting to drill the tank but at least look into the process, it really is that easy. You'll gain a lot of internal space removing the original overflows.
As for the stand-pipes in each overflow box, it wouldn't matter which ones you placed in the respective overflows (use what is most logical in regard to plumbing your sump).
As for the stand-pipes in each overflow box, it wouldn't matter which ones you placed in the respective overflows (use what is most logical in regard to plumbing your sump).