Front brake Caliper and Clutch

I have a couple of issue with my 82 xj650.
#1. I just put on my new front tire and cleaned and replaced the seals in my caliper, i completely bled the brakes with fresh fluid and they seemed nice and firm. When i started going down the road, it's like the brakes are barely gripping, i have to mash the handle to just slow the bike, they have no firmness while the bike is going, but when up on the center stand, i can spin the front tire and the brakes are nice and firm, stopping the tire on a dime.

#2. My clutch seems to shift a little hard, it works but it seems that shifting from gear to gear is just a little too much of a shock, i loosened both the cable at the handle and the tensioner and tried readjusting but i cannot get it where i want it. My Haynes Manual doesn't give much advice on this. There is fresh fluid in the transmission and before i changed the cable it worked fine. The cable is correct as well.

 

#1 is easy - you've still got air in the line. Feeling a firm stop while the wheel is spinning freely is MUCH different than when it's under load - ie rolling.
Keep bleeding that sucker some more.
Also you didn't specify whether they're new pads or not -- new pads need to "bed in" to the rotor before you get maximum braking power.

For #2 - first make sure your oil level is still proper. Remember, these bikes share the engine oil with the transmission, so after an oil change the level will drop once it's been run for a while. Low oil level would certainly cause hard shifting, as the synchronizers wouldn't get enough lube, and would grab hard.
For the clutch, you're just going to have to keep adjusting until you find that "right spot" for you and your bike.

 

I just did the same thing on just the front brake on my 1100, completely drained the old brake fluid out and pulled the piston out of the caliper and had lots of gunk behind the piston.

(Firstly the 1100 has linked braking, the handle lever for the front only squeezes the right front disk, the foot lever squeezes the rear and left front disk.) I've had a problem with my right front caliper hanging and the housing has been rubbing the disk, I found cleaning everything even the pivot slide bolt wasn't curing the problem.

Anyway, samething, on the stand the lever now comes in further giving me better feel and stops the wheel instantly, but when I go out for a ride the brake is just weak. Of course it was weak before too. These older bikes probably weakest part is terrible brakes. Even my 89' Vmax has the single pot calipers but 10 x more stopping power then the single pots on the 82' 1100. One thing you can do you help improve it is re-surface your disks.
More or less if your disk's are shiny, they put up less resistance against the pads. I need to do this myself, although the improvement isn't going to be a huge increase, but it will be better.

You can also switch to braided brake lines, as rubber ones will also bulge slightly, taking some of the fluid's pressure force away from reaching the caliper to push the piston.