Entirely possible that I buggered up the same thing on both motors. If new plugs and wires carefully installed doesn't solve the problem, I'll try the 4-7 wire swap and see if that makes it better or worse. Still waiting on more info from the engine builder - they're not very good about returning phone calls.

make sure you ck coil wires, you said changing wires, had a weird issue 2 weeks ago, twin engine cruiser 454MPI's we on long trip, left coming home engine shut off clean, would not start. went checked, coil wire was out of boot on dist, the whole inside of the center was burnt to dust and finally vibrated out, now these were new merc wires installed earlier this season, totally burnt out...never saw it before..glad we had old set or would have been a very long ride back at 6mph !

.One was down 500 rpm BEFORE removal you said? what rpm you see now?

Based off the backfiring and popping, check the firing order as that sounds very possible.
check timing since it was messed with and make sure you are doing it right anywhere around 34 Total should be ok as long as same, fine tune later. set light to zero if it is a dial and check that way to be sure, some are way off..
check fuel pressure, idling AND under way
spray caps and wires with water and around plugs to check for arc
check plugs after a WOT asap after shutting down will give you idea of lean or rich, cant really just shut it off on a boat like a car, but come off plane asap and shut off.
if you are still way off like before between the 2 do compression test.
make sure you have good voltage 12.5++ minimal
replace fuel filters just for fun to make sure they good.

just a few things to think about..

Great tips - thank you. I will report back after some more work in troubleshooting.

An exhaust cam lobe going flat can cause pop back through the carb as well

Skip is the e-bay parts peddler that put Proccomp on the map.. His uncle Fred White is the engine builder. Separate companies but right near each other and related of course.

Update:
Finally got everything back together and got out on the water. New plugs/wires/caps/rotors. Base timing set to 22 degrees.
My cooling issues have been resolved - the addition of circulating pumps to both motors, instead of crossovers, has brought temps down to 110 on both motors. Oil temps run a little warmer on starboard motor (210 vs 180 at sustained 3500 rpm). With the old setup (crossovers) I was seeing water temps of 190-210 degrees overall and a 40-70 degree differential between cylinder heads.

Max speed I saw was 56mph, and max rpm was about 3700-3800. That was WOT with a good amount of trim. So I'm short about 1500 rpm (rev limiters set to 5200) and 20mph.

Timing was set to 22 degrees on starboard motor and 24 degrees on port motor, as the port motor needed the extra 2 degrees to keep from backfiring through the carb at idle. I did get another mph or 2 out of it after bumping up the timing so it sounds like that may be the solution here, but I'm worried about too much timing at the top end.

After about an hour of running around at 3000-3500 rpm, the port side of the transom and underside of the swim platform was sooty. starboard side was clean.

New electric fuel pressure gauges showing 6-7psi as they should, thru Holley red electric pumps and mechanical pumps on the motor.

Have someone that is a marine engine mechanic look at both engines before you have two cast iron slugs that need to be rebuilt.

The fact it was backfiring at idle, tells me somethings jacked up. 2 degrees of timing shouldnt be the difference of backfire vs no backfire at idle. Ive had engines that idled at 8*and 36* , never had backfire at idle.

either the firing order is screwed up, valvetrain is screwed up, etc. Is the timing pointer an adjustable type ?

Some additional data I forgot to mention.

The carbs (QFT 850) sat on my garage floor for 2 months while the motors were out. There was definitely some ethanol-containing 93 octane in there when the carbs were taken out of service.

During yesterday's run, it almost seemed like the opening of the secondaries didn't make any difference in power. I pulled the throttles back a few clicks from WOT with no discernable drop in power.

22-24 degrees? why so low?? sure not 32-34?

My gun is set up like that, it came that way and never had any issues, eventually I plan to change that, but for now it works fine that way.

That's base timing - before any advance comes in.

These 540s are supposed to be rated at 660 hp, but with rev limit set to 5200 it's probably closer to 550.

I totally forgot to try the 4/7 swap of the wires when I was out on Saturday, unfortunately.

The motors were in the boat when I bought it earlier this year. They had 24 hours on them.

Mine is set up with the electric pumps first, delivering fuel to the mechanicals, then on to the carbs.

I just checked with the builder again - they said total timing needs to be 35 or less, initial could be as low as 12 but depends on a variety of factors with setup. THey were surprised by me needing 22-24 degrees at idle.

if youre setting base to 24*, then how much total do you have !?
also, is the timing pointer verified that tdc is actually tdc

I'm embarrassed to admit that I don't have definitive answers to either question.
I know that I'm *close* to TDC, by observing piston position on cylinder #1 and rotor position.

https://cimg1.ibsrv.net/gimg/www.off...16946a1f43.png
are the plug wires connected as in this picture, doesn't really matter where #1 starts on the cap as long as a the rotor is pointing at it

Any chance the float in the carb is set to high or the needle is sticking and just dumping to much gas in the motor

I personally would ditch the electric pump/mechanical setup. Id run one or the other.

those holley red pumps are crap. Id get rid of it. They dont flow worth a dam ,and if anything are probably a restriction in the setup. They barely support 400/425hp . Then you have tee's , filter restrctions, etc.

id get a decent mechanical pump, run a -8 line from tank to pump, and -8 to carb feed line. Id also make sure the carb has at least .110 needle and seats.

i wouldnt be surprised if youre starving those engines for fuel.

I also thought the mech/elec fuel pump setup was odd. Maybe I rerigged that wrong when I put the engines back in?
My fuel pressure gauges are brand-new autometer electric gauges, the sender picks up at the end of the fuel rail after the carbs are fed, and reads 6-7 psi at WOT. Does this rule out the fuel pump setup being the problem?
Worth noting is that both Holley red elec pumps are less than 10 hours old, I replaced one over the summer and the other one about a month ago. The old pumps had corroded and seized about 2 months apart from each other. One, before I pulled the engines, the other, shortly thereafter.

https://cimg2.ibsrv.net/gimg/www.off...db3752a1a2.jpg
https://cimg3.ibsrv.net/gimg/www.off...34a6cca30a.jpg
In the second pic, you can see the Tee fitting. The electric pump outputs to one side of the Tee, the center of the Tee is screwed into the INlet of the mechanical pump, and the other side of the Tee runs up to the carburetor. The outlet of the mechanical pump runs back towards the forward bulkhead, back to the fuel filter head, presumably as a return?

I've arranged to bring the boat to a highly recommended marine mechanic on Thursday, and leave it there until it's right.

That's a very odd setup to me, you might have 6-7 PSI at WOT but more than likely you don't have adequate fuel flow due to the Mech/Electric pump setup. It appears to me that the mechanical pump is robbing fuel flow from the carb and sending it back to the filter head.

All of the older Cigarettes were setup with an electric pump and a mechanical pump from the factory.

I thought this looked factory. Question is whether I rigged it all correctly after the R&R of the engines.

Correct, the SSM and TRS boats had a booster electric fuel pump that ran when the engine would crank and as long as the oil pressure was over 20 PSI. The Electric pump sent fuel to the fuel filter/separator, then to the Mechanical fuel pump, and from there to the carb.

That plumbing doesn't seem correct, what would the mechanical pump be used for?