On the new floor it's worth putting down 1.5" XPS insulating foam (R7.5) on the floor and securing the new subfloor to the slab with TapCons 24" o.c. rather than repeating the 2x4 sleeper mistake. This makes the floor warmer and less susceptible to mold/rot issues, as well as saving on the heating bills. If there is no vapor barrier in the slab (or if you don't know), it's cheap insurance to put down 6-10mil poly sheeting under the XPS as both a slip-surface and vapor barrier against ground moisture. At current natural gas pricing this is not strictly a financial return on heating costs issue (though it does have a long term financial rationale, see Table 2, p10- you're in climate zone 4) but it's huge on comfort and indoor air quality (by keeping the mold spore counts down.)
It sounds like the original system is a "mono-flow Tee" configuration, in which case plugging lopping the Tees and going with a direct flow approach may lead to room-by-room temperature imbalances.
Replacing sections of corroded 1.25" iron with 1" copper has negligible effect on flow, but if you're re-configuring to a lower-flow rate and series-plumbed radiators rather than a mono-flow Teed setup it's unlikely you would need anything bigger than 3/4" PEX. Even if you leave one zone as monoflow it's likely that you'd still be able to achieve sufficient flow with 3/4" PEX if it's just running between the boiler and each end of the pre-existing (now shorter by half) section of mono-flow, but leaving it at 1" wouldn't hurt.
Going with two boilers instead of one is likely to leave you with TWO boilers oversized for their loads, whereas if you actually did some design work up front (there's a concept for ya! ;-) I wish more pros actually did that in the northeast. :-( ) it would be cheaper and more efficient running it as two roughly-equal zones on one boiler (probably set up with a separate pump on each zone rather than one monster pump and high-flow zone valves.)
All good heating system designs start with a room-by-room heat load calculation (ACCA Manual-J, or even I=B=R is good enough for a house this size in your climate), using realistic indoor and the 99% outdoor design temperature for your location. (For most of the Sandy-affected areas of NY & L.I. using +15F as a design temp would work.) Without that you have no idea how much radiation or flow you would need in each room and zone, or what size boiler would operate most efficiently.
If experience any guide it's likely that the existing boiler is probably more than 2x oversized for the actual heat loads, so it's not really a great guide. If you oversize the boiler it will suffer efficiency losses from cycling, and incur higher maintenance costs to boot. Now that you're breaking it up into two zones, oversizing issues loom much larger, since you now have less than half the radiation available on the smaller zone that needs to be able to deliver 100% of the boiler's heat to avoid cycling. But if you use a high-efficiency modulating-condensing boiler right-sized for the whole-house load, most of those have at least a 4:1 turn-down ratio, and will simply modulate it's firing rate to match the load. But a mod-con boiler at 3x oversizing may still have real problems managing single-zone calls efficiently.
You also have too look at the total radiator sizing on each zone/room relative to it's load, since that determines the maximum temperature required to deliver the heat, and how low the water temp can get without causing excessive on/off cycling on the boiler. Mod-con boilers all come with "outdoor reset" controls, that use the outside temperature to determine the output temperature of the boiler. This is done to increase the efficiency, which is maximized at the lowest water temp that doesn't over-cycle the boiler. You can't get any better than ~87% efficiency out of a condensing boiler if the water coming back from the radiators is over 125F or so, which isn't going to happen with 180F outbound water. But with 110F return water it'll be in the mid-90s, and with sub-100F return water it can hit the high-90s. High-mass old-school radiators are GREAT at delivering predictable heat at lower temps, unlike fin-tube baseboard, so this is probably going to work out pretty well if you design it right.
The real answer to your pipe sizing question will fall out of the flow requirement math based on how you configure the radiators and zones, and the lengths/pumping head the loops present. In most series-plumbed situations 3/4" is going to be fine after all design-ducks are in a row, but as I stated earlier, you'll probably need/want to leave it as a mono-flow Tee, otherwise the heat balance will be all over the place, since the temperature of the water entering the last radiator on the loop will be 10s of degrees colder than the first one in line. But with only half the radiators on a given loop it won't need the original flow rates to work well, and if it's only a few 10s of feet of PEX to hook up the loop, that may still work at 3/4" without resorting to a ridiculous sized pump. (I imagine the original pump is a pretty beefy sucker, not a Taco-007 or similar.)