Longer bolts won't make a difference. They only need to be as long as the height of the material being bolted. Any longer is just excess.
The interference of the parts is true in part, but the bolt still has some sheer aspect to it also. As for spacers, the ones I use are the same diameter of the ears on the knukles at the flat spots. This is usually about 1.000" on most kits.
Welding them in place won't do all the much for you and in fact if you get them too hot you may warp them as they are put in place. We shim calipers all the time and so too do many Wilwood kits, just like your cam sprockets they rely on good clamp loads and interference of the parts.
Sorry to say it, but my money is on one of them not being tightened properly or some debri preventing it from being seated all the way. Be sure the surfaces are clean and free of burs.
