Hey guys, have an issue with a 98 eclipse GS 5 spd.

Car will not shift when running, will shift fine when off. I read the site and figured it was either slave or master cyl related, so i checked and sure enough , master was leaking. So I replaced master and slave both and bled them. issue is still occurring and clutch pedal still feels soft. pressure is firmer than it was before, but still not shifting when running. Any ideas? I really dont want to have to repalce the clutch if i dont have to, and honestly i have neither the tools or the space to do so. so to sum up..

Replaced master and slave.
Bled system
No air in lines, nothing but clean clear fluid out of the bleeder valve, no bubbles.

car shifts fine when not running, but will not shift at all when running.

Any help or ideas on what to check are appreciated.