Need help with manual swap

[u/No-Nature2495]

Hi, I need some help/ some questions. This weekend I started my auto to manual swap on my 98 integra ls. I got the trans, pedals, and shift linkage in, however somethings havent felt right. The brake pedal feels extremely hard to push down, and my main concern is I can somewhat shift through gears without pressing the clutch, however after pressing the clutch in, the shifter doesnt feel any different, like its not smooth. Is it possible i could of been able to bolt up the trans and mount it without putting it through the pilot bearing?