Troubleshooting an acceleration bog/hesitation

Background: 1989 Ski Nautique 2001, original PCM 351 with just over 500 hours, Holley 4160, prestolite distributor with breaker points, initial timing is 10* BTDC at ~700 RPM. When I bought the boat last fall, it didn't want to idle, especially when warm, so previous owner had cranked idle speed up (I think it was around 1000 RPM or so) I think in an attempt to compensate. Also had an off-idle/part throttle hesitation or bog where the engine wouldn't respond right away when either taking off under hard acceleration, or when getting back on the throttle after slowing down. I suspected the idle issues were due to a vacuum leak around the carb base/spacer, and indeed when I got the original cast iron spacer off and started to machine it flat it was pretty obvious it was a ways out of flat. So I ordered a new phenolic spacer from Summit, and the thick carb gaskets from Skidim, which I think is what fixed the idle issue. But I also rebuilt the carb while I had it off the intake with a Holley marine rebuild kit from Summit, did not find any clogged passages, and it was pretty obvious someone had been in there before me, lots of tool marks from scraping and such on gasket surfaces and passages on metering block and carb body. Got it all back together and it ran much better, no more idle issues when warm, and no longer noticed the hesitation. One problem fixed, but now noticed that my idle speed would hang up after a hard pull until I'd shut the key off and turn it back on. Mostly with the help of searching this forum, I traced this to the secondary butterflies hanging up, due to a loose return linkage, probably because previous mechanics had to adjust it when they cranked down the primary curb idle screw to compensate for the idle issues. After reading some more about carb tuning and such (always a dangerous thing), I realized that I probably didn't set up the primary butterfly position for proper transfer slot exposure, so wanted to pull the carb back off anyways to check and adjust. Readjusted primaries to just expose the small square of transfer slot, and just barely had to crack the secondary off the stop to get the idle speed right. And after bending back the secondary stop linkage, my idle now returns back down to 700 ish every time. Yay. Fast-forward to...

The problem: I am now noticing quite a bog/hesitation on a hard acceleration from idle, and to be honest I'm not sure if it has been there the whole time or if I'm just now noticing it, as I hadn't had the good fortune to pull an adult slalom skier out of a deep water stop until a few weeks ago. What happens is, if I start at idle and just "drop the hammer", the engine just starts to accelerate for a split second, and then stops suddenly for a second or two, then catches up and pulls hard. It feels as if someone actually pulls back on the throttle for a second, then slams it back forward. No audible missing or backfiring, no black smoke, just seems like it loses power for a second or two. The boat otherwise runs fine; will pull up to 47 MPH on a GPS speedometer, idles fine in and out of gear. I can repeat this without a skier in the water too if I just throw the throttle down hard to try to accelerate as fast as possible (in gear only, throttle seems to respond normally in neutral and will rev nice and crisp).

What I've tried: I checked timing with a timing light, 10* initial, and I do see it advance smoothly as I rev the engine. Pulled breaker plate off distributor and inspected advance weight operation, they seem to move nice and freely without binding. Points gap set to .018, new points set and condenser last season (a story for another day, I had originally put an EI module in there, reverting back to points fixed another weird issue I was having where the engine would feel like it would "skip" occasionally when cruising), timing checked after adjusting points of course. Also played with moving timing up or down but the engine seemed to want to idle best around 10 so left it there. I did check for vacuum leaks with some carb cleaner around carb base after the last time I had the carb off to adjust the primaries, but admittedly I need to do a more thorough job of this (with a spray bottle of water this time probably as I've learned since then). I did adjust the idle mixture, but only in the driveway, have NOT had a chance to do that in gear like I know I should yet, will do that this weekend when we take the boat up to the lake for the week. In neutral, they do seem to like to be the default 1.5 turns out though, and if I turn them in much more than that the engine tries to die on me, so I know the engine is idling off the idle circuit and so I think the mixture screws are responsive enough (this also got a lot better after I had re-adjusted the primary butterflies to expose less of the transfer slots, and idle also feels a lot strong in gear now with this adjustment).

What I know I have left to check: I've been reading a ton about what causes hesitation in these engine/carb combos, and of course all this sounds like a problem with the accelerator pump circuit. So I've verified that my accelerator pump linkage is adjusted so that the pump arm is touching the linkage at idle, and that there is no slop between the throttle linkage and accelerator pump arm (i.e., the pump arm moves as soon as the throttle is moved). I get a good squirt of gas from both nozzles as soon as I move the throttle from idle, so that adjustment seems to be okay. However, I did notice last night that the pump cam (it's the white colored cam, FYI) was set on the #2 position as opposed to the #1 position. Based on my reading, the #1 position should be used for idle speeds <900 RPM to bring the full lift of the pump cam in sooner, while the #2 position should be used for idle speeds >900 RPM to delay the lift profile of the pump cam to compensate for the higher idle position. I assume that the pump cam was moved to the #2 position by a previous mechanic to compensate for the high idle speed, but who knows. I moved it back to the #1 position last night but haven't had a chance to water test yet. I think my expectations for this having much impact are low though, since most folks seem to say that pump cam adjustments can help you go from good to better, but not from bad to good. I also need to retune the idle mixture in gear, but the boat does shift pretty nicely in and out of gear now without much change in idle speed so I suspect this is fairly close as-is, and since this should only affect the idle characteristics and not so much the acceleration, if I understand correctly, my expectations are also low for that adjustment having too much impact. Please correct me if I'm wrong! I also haven't tested with a hard pull since adjusting the secondary stop linkage; I don't expect this will have a big impact, but I had thought that when that linkage was loose, maybe that would have allowed a little more air into carb leaning it out a little when the vacuum dropped on a hard pull before the secondary circuit actually kicks in. 

So next up is a water test to check performance after the adjustment to the secondary stop and the accelerator pump cam position, then adjust idle mix in gear and re-test to rule that out. What am I missing? Any other ideas? Since the boat seems to run strong up to 47 MPH at WOT I don't really think the fuel system (before the carb) is to blame, but I did recently replace the (very scary and degraded) fuel line, the fuel/water separator (replaced the old black and orange FRAM can with a spin-on canister type), and the anti-siphon valve was checked last season (but haven't had that apart yet this season since I haven't had reason to suspect it).