your comment "Swift is primarily intended as a resource for fatigue analysis of skin repairs ..." lead me to think that you were also concerned about the static strength of the repaired joint. my post was saying that for static analysis you don't Need to consider the fastener stiffness; from the ultimate strength point of view the outer fastners will yield and load will redistribute untill all the fastners are working at the same level.
from the DT perspective, unless you're upsizing the fasteners, or extending the splice, there shouldn't be any significant change in the distribution of load transfer out of the terminating member; you'll have the same number and size of fasteners. One thing you Could consider is that you've changed the inspection of the less critical fasteners on the splice (by covering them with the repair angle) ... the structural inspection program of the splice is going to be based on the most critical end fasteners, but should require inspection of all the fasteners. now that you've added the repair angle (on top of the splice) you'll need a different inspection procedure to inspect the splice.
if you are changing these (the size and/or number of fasteners), then the job is quite complex. yes, as planedr notes, there is a procedure in Niu and you can build a compliance model ... it is going to be complex, and take some time, and the biggest factor affecting the analysis will be the bolt stiffness model you assume (Swift, aka Douglas Aircraft, and Niu present very different models). Niu presents quite a nice fatigue analysis (determining an effective Kt including the effects of load transfer) which you may use as substantiating the threshold inspection (some certifying people like this, some don't) For the repeat interval, didn't depend on how big the detectable damage is. if it is large, then you could rationalise that the situation is unchanged by the repair (that the crack would make the end fastener ineffective). if it's small then you'll need to do a crack growth calc as well, which if you're new to DT and repairs isn't something to be expained in these forums ... it'll take too long to go over all the considerations.
i'd suggest that there are many ways to rationalise your solution without a detailled analysis, and if you're in the repair world you're probably already late. i sympathise, you're in a difficult position; repairs need a lot of experience to understand the significant features and you never time for analysis you don't Need. it sounds like you're fresh out of school and doing the best you can with the resources available ... your company should be helping more.
good luck