B737 Captain reports difficulties with aircraft automation while attempting to intercept the LOC Runway 27 at SAN.

Narrative

After planning a LOC Runway 27 approach into SAN using VNAV/LNAV; previous aircraft reported heavy precipitation return at base leg point. We requested turn prior to or after passing cell. SOCAL gave us a 90 degree intercept heading of 180 degrees. LNAV was selected. ATC then changed the intercept heading to 240 degrees and cleared us to intercept the LOC; maintain 4000 FT until established; and clearance for the approach. I erroneously armed the VOR/LOC; selected heading 240 degrees; and noted that the course would intercept inside of VYDDA. I entered a leg intercept to OKAIN and selected LNAV prior to wings level causing the aircraft to reverse the turn. I turned back toward the 240 degree heading causing reversion to Control Wheel Steering; over banking to intercept the LOC course due to strong tailwind. Reacting to turbulence; I reverted to Control Wheel Steering and descended below the OKAIN step-down altitude of 3600 FT. Copilot notified me of over bank and reset altitude alert to 3600 FT as SOCAL advised that we were below MVA. I began correcting to 3600 FT but did not achieve it before crossing OKAIN and descended manually on VNAV path using vertical speed until inside REEBO and broke out at about 1500 FT. A stabilized final segment and landing were accomplished as visibility improved to above 6 SM. I should have reverted to manual control more quickly and raw data before assessing the downgraded automation while the guidance was being rebuilt. I became overloaded and allowed scan to deteriorate. Fatigue was a factor; this being day 4 of a 4 day trip with the 2 previous days each of which was 7 hours block in challenging weather. I had planned for Copilot to fly this leg because I had just completed a Category II HGS/AUTOMATIC in challenging weather the previous leg but decided to fly the SAN leg to accommodate the Line Check. Weather and ATC contributed with deteriorating visibility and tailwind (SAN had just switched back to Runway 27). ATC did not account for the heavy precipitation returns on base leg and the tailwinds due to radio congestion; but ultimately I accepted these conditions and made procedural errors that resulted in being as low as 3100 FT; before correcting to 3400 FT as we crossed OKAIN and over banking to achieve LOC course.