trial by error is all you can do, i haven't strayed from the stock rom yet (soon will though
). Just my two cents. Knowing now that it was something in the rom, I'd either
a) try a completely different rom,
b) reinstall your favorite previous rom, and then immediately install that resetunreadcount.cab (i've actually installed it and reinstalled it multiple times just to make sure that if the problem resurfaced, at least it wouldn't be that. Than start sending multiple texts from a friend, yourself, zipwhip, etc.
c) leave the sprint rom a short period (a couple days at least), no additional software installed (just the bare stock rom). Then if all works out, start installing your favorite apps, and if the problem resurfaces (process of elimination). Weed it out, one app at a time.
The good news is you've made some progress by stepping back for a second. Of the three I'd recommend installing your favorite apps on the stock rom. Knowing that your sms messaging is functioning properly on the stock rom, rule out any unruly apps first before you flash a new rom. If you don't do that, you won't know if the problem is in the rom or in the app. Once you know the apps are good, flash your favorite rom and before filling it with your self-certified working apps, send yourself some more texts in the various manners i mentioned. Once you certify the ROM is good, add your Apps and cross your fingers, it should all be good by then.
P.S. When you start installing apps, leave them on the default settings for a while, til you can rule out the app is good, unless it's creator recommends particular settings for your phone.
I try to stick to common apps that i know everyone else is using here on PPC or at XDA that way i can run a search if i have any issues.