It's pretty easy to stack up modifiers on ranged attacks (Point Blank Range, Single Shot etc) and the target number can even be above 100, but is this possible? Or the upper limit is 100? This matters when determing DoS, so I'm just wondering is there a limit on stacking modifiers...

Page 22 of the core rulebook, where it explains how tests work:

Likewise, if the result is 100, then the test automatically fails, even if the target number is greater than 100.

Page 24:

Regardless of the source or combined sources, no final bonus can ever exceed +60 and no final penalty can exceed –60.

I don't think that's quite what the OP meant, but I could be wrong. From my understanding, the question was how to deal with an effective stat that exceeds 100. For example, 60 BS + 60 in bonuses would have a target number of 120, yes? Would that 120 get knocked down to 100, or could it remain at 120 for the purposes of calculating DoS? A roll of 99 is normally pretty bad, but that's still a "decent" roll if the target number was 120. Personally, I see no reason to trim off everything over 100.

even if the target number is greater than 100.

Answers that part of the question too. So cps did answer everything after all

Again, I don't think that's quite the answer the OP is looking for, but that's an assumption on my part. [cps] explains what to do with a "die roll" of 100 (instant, non-negotiable failure), but not a stat that exceeds 100. Bonuses cannot exceed 60, but can effective stats go over 100? This is what I believe is being asked, not about the dice rolls and penalties themselves.

I don't know about actual stats, but effective stats clearly can, and since the OP is talking about rolls and whether it's possible to have TNs>100, I thought it was clearly answering the question, but ultimately only the OP can answer that.

Yeah, I believe the OP was asking with regards to factoring in DoS.

Ie:

Acolyte with 64 BS, manages to rack up +60 to hit with a full auto attack (ie. Effective BS of 124).

Acolyte in question rolls a 53.

Is this considered to be 6 DoS, or is it 8?

Taking the rules at their face value (a big assumption, given FFG, I know), it'd still be one for succeeding plus the tens digit (12, in this case) of the TN minus the tens digit of the role (5). 1+(12-5)=8.