Things to look out for when trying a multitude of games. As you probably know all the switch settings can vary wildly between games. One which can cause no end of confusion is the alarm on power up but it takes about 30 secs before normal play will commence. The actual switch to turn it off probably varies between games. Don't you just love MPU3?
Your reel fault without the alpha was showing 3 (7 seg) and I would expect hold 3 (reel C) also to show. There's loads of reasons as to why you can get a reel fault as you probably know. First port of call would be, are all the lamp sensors working? Make sure all the bulbs light up during reel spin, I'm sure they are but if not T55 (BCX38) is your main suspect if none light up. Sensors do fail of course and the best way to prove a fault on the reel deck is to swap the cables on the backboard and see if the fault goes to the other reel.
Are the reels stuttering? If so possible bad red cable or dry joints on the red socket. It's a good idea to check all the sockets for dry joints and if you find any on a socket resolder the whole socket. Next thing is failing reel drive transistors (all BCX38) or failing drive chips (74LS04) and even worse failing 6821 (IC5).
When you swap out D44/45 replace them with modern P600 types and not IN5408's as some folks do. I find they don't get anywhere near as hot as the old types did so lead curling isn't as important as it was. No harm in doing it though.