You say that - I was around in that era. And my batch files for boot really pushed the boundaries of what was possible (PC Magazine AMENU, CHOICE, 4DOS, etc. etc. etc.), we were constantly shoving hardware in and out (ah, the joys of top-opening hinged, unlocked PC beige cases!) and yet I never once had an IRQ conflict. It's not hard... Soundblaster on 7, everything else on default (given that you went for IRQ 5, and CDROM.SYS there's your problem!).
P.S. I had a boot menu, from which you then selected a config, which then loaded config.sys/autoexec.bat as appropriate, and you could get anything from 638Kb of free RAM (with just mouse and MSCDEX and a lot of loading-high and other tricks if I remember rightly) through to a FORTRAN environment with RAMDisk, EMM386, etc., on especially for certain versions of Windows (3.1, 3.11 with networking , etc.) and a handful of specific-game ones that were really finicky about exact configurations to work properly. Even one for a parallel-port daisy-chain which, with the right TSR, pretended to be a (slow) IPX-capable Ethernet card which we used to game over using Quake! We upgraded to 10Base2 and then T eventually, though...
It was hilarious on an IRC forum once when someone tried to convince my brother that he'd got into our computer and "could read our AUTOEXEC.BAT". Go on, then, we said. Show us. He just copy/pasted the default MS-DOS one, and we fell about because our AUTOEXEC at that point called something like 20+ other batches files and had text menus and all sorts in it. Obviously he wanted us to "run this program that I'll DCC you to fix everything so other people can't get in".