Trying to replace the seal at the upper sector shaft part of the box, To get the dust cap off i understand you have to spin the shaft with the Allen key fitting to the right, I was wondering if i have to separate the pit man arm from the suspension as it is getting pretty hard to turn and i DOn't want to hurt anything if possible, Thanks for the help.

You talking about the sector shaft cap? Just remove the bolts on the cap, DON'T, touch the adjustment bolt.

Once it's off, remove the adjustment bolt, but count the turns needed to get it out. Replace the o rings and reassemble, turning the adjustment bolt back the same number of turns.

There are no bolts, mine has the round dome shaped dust cover, the manual says to turn the shaft bolt clockwise, it has a Allen head recess at the end of the shaft

Ok, not the box I was thinking but, unthread the cap and don't touch the adjuster screw.
Actually, you've already thrown off the adjustment so back in off again for now, you'll have to readjust after resealing.

Remove cap and adjustment as a unit, replace seals. Install adjustment so it's bottomed out in the cap. Install cap on box. Reset adjustment screw per manual.