So I am choosing a stem for my new build. I have a really nice 90mm stem I love however I'm not sure if its will be too short. The background info is my last bike (Italian road semi aggressive geometry) had a 54cm top tube with a 100mm stem. It was pretty comfortable never really looked into changing it. The current build has a 52cm top tube is aggressive Italian geometry and is going to be more a racing bike. Do you think a 90mm stem of average angle will be too short?

I hope average angle means level with the ground. You are shortening the reach by about 30mm assuming the stem isn't angled too far up. You will notice a difference. I think you will feel cramped on the new bike if the old one was comfortable. Try it but be ready to find a new longer stem (and rewrap the bars).

By average I mean around 75-80 degrees. It's down but not pista down. I agree I will prob have to experiment a little. Maybe if its lower than I had the last one it will be better. Comfort isn't an issue. Control and performance.