a cloth af 51 + base af caster shield = 102 af. compared with a heretic without armor items with only a spec af (heretic shield buff is spec a spec af buff, thats special about this class) that gives you 517 af / 5 => 103.4 af. the result is that the heretic does not get any use from that spec af buff. i am guessing that: AF = AF * (item level) / (max item level). so if your item level = 0 you get zero bonus from spec and base af.
if i compare a cloth caster with base af and a spec af buff with a heretic with the same cloth armor + his own spec af with the amount of buffbonus so that you get equal af. the damage values match each other. so there is no difference between the af from a base or spec af buff.
and finally some testing on toa af bonus that is really looking deadly to me... test subject is a rr13 heretic with 25% buff bonus and 50 speced in enhancements. using pd9 and 26% item res + 5% res from the shield +3% class resist + 6% mythirian = 40% primary + 30% sec res => damage * 0.42. the values i use for this test are the resistances, that's why they are so high. the lvl 75 hits me slash mob hits me for 511 (- x) and the x i am using here (because its not caped and gives me big numbers to see small differences

). i only post the min damage values here:
naked + sitting: 3315
naked: 2000
naked + 50 toaaf + baseaf + specaf: 1333
naked + baseaf + specaf: 2000
naked + sitting + 50 toaaf: 2210
naked + 40 toaaf: 1428
naked + 25 toaaf: 1600
1) as allready said, if level 0 armor = naked => baseaf and specaf have no influence
2) sitting gets extra damage
3) toa af must be calculated total different then baseaf and spec af because it has a influence on damage in both cases, naked and naked + sitting.
4) doing math on this toa af effects the damage with: "DAMAGE = DAMAGE / (1 + 0.01 * TOA_AF)". so that 50 toa af are reducing the damage you get from 100% to 66.66....% or you can also say its like a plate armor...
sure i need to do more testing on toa af and how it works if you have armor equiped but still this is a very huge impact.