I just noticed this post. When booting via 2 stage, WinPE can not see the 2nd stage ISO without a special driver. My guess is that your customizations are not stored in the boot.wim file but rather just on the ISO file system. So, you could either move the customizations (and anything else you need access to) into the boot.wim file. Or you could try to add a driver that can expose the 2nd stage ISO, such as firadisk or winvblock
I've successfully used Firadisk 0.0.1.30 for this purpose (FiraDisk (latest = 0.0.1.30) - FileDisks/RamDisks: Firadisk, etc. - reboot.pro) with WinPE 3.1 32 & 64 bit. When I did this I found that using DISM to include firadisk did not expose the 2nd stage image. Maybe I was doing something wrong. What did work for was me was to place the firadisk drivers in boot.wim at x:\firadisk\ and then loaded them via startnet.cmd with "devcon install x:\firadisk\firadisk.inf root\firadisk". With that, WinPE could see the 2nd stage ISO. Note that this may or may not work for you. I have no experience with Win7SE. Good luck if you try it, and please let me know how it goes.
BTW - if this were my imaging scheme I would place my tools and custom batch scripts on a network share. In my WinPE I'd have startnet.cmd map the share with the net use command and then call the batch scripts and tools from there. This way the PE image is as small as possible for faster booting and I could change the tools and scripts without changing the PE image.