Just adding a little update here. After plugging/unplugging the A & B boards from each other several times the board started working without any glitchy bars in the background sprites. Once it was confirmed working I installed my Darksoft multi kit board on the USA CP2 board that was originally Xmen vs Street Fighter and had the same issues with the connection between A & B boards. Several connect/disconnects later everything started working. That was yesterday.
Following that, today I thought I should retest my other CPS2 board that I thought I had fried (the reason why I bought the xmen vs street fighter board in the first place). I did several connect/disconnects and it started playing fine but with bars in the background sprites. At this point, I'll get some cleaner to clean the pins connecting A & B boards so that I can give it another go, but I feel confident my Astro didn't fry any boards it it was just the connection between A & B boards all along.