First, is it Clays or Universal Clays? IMO, Clays is a terrible 9mm powder, too fast. So 125gr what, lead, plated, jacketed? Yes it matters. It sounds like Universal Clays, good 9mm powder. IF it is Universal, then 3.5gr isn't even a starting load for lead bullets so really doesn't work for jacketed. This is likely the problem w/ the gun not functioning. That could also be the accuracy issue, but proper die setup is important. Over crimping is often the culprit of poor accuracy. The bullet is swaged down in size by the crimp & ruins accuracy. Particularly bad w/ lead or plated bullets. The crimp should not be visible to the eye. If in doubt, pull a bullet, if it has a ring around where the case mouth is, it's crimped too much.
Barrel length in service pistols doesn't matter much as to what powder to use. Look at your several manuals, find the vel level you want & a powder that will get you there w/o pushing max loads. I start w/ average middle data, it is more likely to run the gun & give acceptable accuracy. Load NO MORE than 10rds with that load, then increase charge wt 0.1gr & load 10 more, upto average max data. Shoot them in order, note functioning, accuracy & any perssure signs, low or high. Some place in there you'll find the load your gun likes. This is called load developement or load work up. It's the proper way to approach reloading, gives you the most useable data with the least effort, time & cost. Picking starting data & loading 100rds is a sure date w/ your bullet puller. You have much to learn grasshopper. Go slow, ask questions, just make sure you give us enough info to give a decent response, otherwise it's all just a WAG.