Again it is a '72 with steel fork legs and rusty fork tubes, for a cost effective fix, what would be the best front end (off another model) for the old girl?

Like Dale suggested, I also have S3 forks, clamps, and rim for the simple upgrade, but plan to mod the upper clamp to retain the 72 gauges.

Pipes are dinged and stained, what pipe options do you like?
Has anyone been able to find stock pipes that are worth installing?

Though decent used S2 stockers don't seem as pricey as their bigger counterparts, +1 on Jim's clones.

Motor mods?

I'm planning on installing Moo's reeds in my S2 motor. If money will allow, I was thinking of also looking into some port matching and porting, and also combustion chamber work from Scott Clough Racing here in CA, like Tim Steele had done to his S-series not too long ago (matching and head work I believe).

Is the 4 bearing crank that much of a problem?

I believe the Service Bulletin stated updating to a 6-bearing was more a precautionary measure.

Can you retrofit a 6 bearing crank?

Again referring to the Bulletin, if I recall correctly, you just need to drill 2 additional oiling holes in the upper case half to provide proper oiling to the 2 addtional bearings.

Electronic ignitions?

I still have a Boyer Brandsen in the box and will likely go with that. M in SC also adapted a late H1 iggy to his 73 S2A if I'm not mistaken.