Hi Andy, sorry to hear about the loss of your b25.
I wouldn't worry about running slightly less aggressive tune. Better to be safe than sorry. You are gaining a lot of torque by upgrading to longer stroke b30.
Now some advice from a guy that did the exact swap (but I went from b25 stage1 to b30 stage2).
I suggest you install the engine without the supercharger and make sure it runs well first. Smoke check, fuel pressure test etc. Drive it around for few weeks (with your stock 325 ECU is fine).
Your spare engine will likely come with intake manifold and TB. You will still need the b30 airbox and MAF (make sure you get the right one for your ECU (MS45 vs MS43))
Replace stuff that's difficult to get to while the engine is out - OFHG, oil pan seal, rear crankshaft seal, hard plastic pipes for the cooling system. Everything else is easily accessible even with the SC installed.
My gauge never goes over 10PSI (b30 TS2). If the tune was too aggressive you should have heard pinging under heavy load.