For station:

 1. ALT-F12 \ Physics \ Thermal -> slide Radiation factor to maximum.
    Should help with heat issue.
 2. Use time warp to remove wobbling.
 3. Position station docking port closest to station CoM axis toward normal or
    anti-normal (magenta triangles). That way even if it time passes it will still point north/south instead of running away from your capsule.
 4. Time-warp again to remove residual wobbling.

For capsule with MechJeb:

1. ALT-F12 \ Physics \ Thermal -> slide Radiation factor to maximum. Should help with heat issue.
2. Get to different orbit, lower orbit will save Delta-V. Higher is preferable when target is below 80km due to atmosphere. (You probably can skip this step)
3. Match planes with target. (Half of issues with docking comes from difference in inclination)
4. Hohmann transfer to target. Yup, it works great for orbit rendezvous with crafts as well.
5. Fine tune closest approach to target.
6. Match velocities with target (at closest approach to target). Now you should be pretty much in same orbit, stable enough for spacewalk for long time.

With target docking port in stable position and orbits matched by MechJeb docking should be easier/safer than automatic. (MechJeb hates my solar panels >.<)

And remember, there is always [The Claw][1].


  [1]: http://wiki.kerbalspaceprogram.com/wiki/Advanced_Grabbing_Unit