If there is one bush I wouldn't replace with poly it would be the box mount, whilst in itself it won't generate the vibes it will transmit them into the car shell a lot better than the std mount, which is what I use.
Is the shake/shudder defo this or a misfire ?, as this will cause vibes but different from other vibes.
Try putting the car in gear and with clutch down revving it to 3K, any difference ?, it sounds like a trans vibe, ie worn gearbox bearings, you could also drive at 50 mph snick it into neutral and rev to 3K to see if the vibes are still there, try it with clutch engaged and disengaged.
tabetha