You totaled the time Shepard and company have spent around indoctrination-capable reaper tech as approximately 3 days. I think that's a fair baseline total.
You also pointed out quite accurately that we don't really know what level of reaper tech is required for indoctrination to occur. I'll accept that as truth as well.
A third point that I didn't see addressed (and that may very well be buried in the codex) regarding indoctrination: Does exposure need to be continuous? Or does excessive time away from the indoctrinating tech allow your body to recover? (I'd love an answer to this from anyone, actually)
Anyway, all those points being acknowledged, I'd like to focus on the second. "We don't know what level of tech is required".
If I remember correctly from the codex, there is no distinction between rapid indoctrination and the slower form aside from the rate of application and the end result (husk versus a slow transition that is slightly more 'normal' in appearance and function, until it eventually becomes a husk anyway). If that is the case, and further assuming that devices designed to indoctrinate rapidly don't require you to actually be impaled on them to work (and I will present evidence to that effect shortly), then Shepard and company have actually been exposed to far more indoctrination than the 3 days you've accounted for.
I don't believe impaling is required for a few simple reasons: The ardat-yakshi monastery being most significant. Samara's daughter (who's name escapes me) was not impaled, and was clearly undergoing rapid indoctrination. She had not reached the end-stage yet, obviously, but it seems silly to assume that she was the only one undergoing the slower form when the reapers were clearly there to harvest additional forces. To account for her presence, and the clearly varied rate of indoctrination, I would theorize that there was a device planted in the monastery capable of rapidly transforming those near it, which would allow for some to be indoctrinated faster than others, and explain the two who survived (mostly) whole. (It casts a bit of a shadow on the other daughter's decision to stay behind, but it makes more sense than assuming that the first daughter was indoctrinated by some slow-indoc device while the other ardat-yakshi were all impaled. 2 devices is harder to accept than 1, and from a tactical standpoint makes less sense.)
That being said, it would seem like a simple jump to assume that ALL indoctrination-capable devices function in the same way as object rho; their presence begins the process, and no direct contact is needed.
Of course I need to account for the geth devices, which is actually rather simple: The writers didn't have indoctrination in mind that early. I had originally written a long-winded explanation of how sovereign didn't have access to rapid-indoc(RI) tech and had the geth make some facsimiles here, but we all know what really happened.
Anyway, moving on... So here we have RI-tech capable of indoctrinating those in close proximity, in my theory. From a tactical standpoint this makes sense: impaling dead enemies is less effective than slowly transforming enemy armies into your soldiers. It still isn't an all-encompassing I-Win button for a war because we simply don't know the range of the effect, or the maximum speed RI occur. Perhaps these devices are also too big to move(a safe assumption, I think. Even the impaler-RI tech wasn't exactly mobile), further limiting their combat effectiveness and giving a need for places like the ardat-yakshi monastery, where the reapers can 'farm up' troops.
Bah. I'm going to run out of time.
I think you see where I'm going with this, though. If my theory is correct, we really don't know how much exposure to indoctrination Shepard has seen. Since we both A) know it to be higher than average and

don't know where the event horizon lies, we can't assume that Shepard is NOT indoctrinated.
The current indoc theory is largely sensationalized and hardly scientific, yes, but it's also not entirely illogical. It's suffered under the weight of days of wishful thinking and desperation, not to mention literally EVERYONE adding to it whenever they saw anything that remotely resembled indoctrination... but that doesn't mean it's core is completely wrong. I'd love to debate this more, as I've spent a bit of time distilling the theory into more likely pieces, and debunking the sensationalist garbage... but I don't even have time to spell-check this and make sure I'm not rambling.
I'll try to come back this afternoon and do a better job of explaining myself, if there's cause to.