Recirc or not shouldn't make cyl 3 misfire especially when not in boost, it sounds like this is an all the time misfire and not just an on boost misfire. Nor should a different MAF make one cylinder misfire.
May also be worth while to try swapping the resistors between injectors, double checking they're all the same resistance, and swapping the injector between cylinder positions. I like to swap parts over more than one cylinder, like if Cyl3 is the issue I'd swap it to cyl 1 not to cyl 2 or 4. That way it's further away from the possible problem and you can more solidly know if the problem went with the part or the problem stayed with the cylinder. One more thing to consider would be the possibility of Cyl 3 being lean due to a vaccum leak at the injector or the intake manifold port on the head.
So if this were in my bay at the shop I'd do things in this order to diagnose a misfire.
0. drive vehicle to ascertain exact conditions of misfire, all the time, only at idle or only under load, hot/cold, etc.
0.a verify which cylinder is misfiring by pulling plug wire or injector connector while engine is running if it's an idle misfire, have seen engines with multiple weak cylinders throw misfire code for wrong cylinder due to slowing and speeding crank shaft speeds. Usually the actual misfire is the cylinder before the indicated misfire in the firing order when this happens, seems to most commonly be a Ford issue.
1. check spark with plug out of cylinder and grounded to head to verify plug works and coil works.
2. check compression on cyl 3 and cyl 1 for a comparison, if needed follow up with compression check on cylinders adjacent to problem cylinder to check for compression bleeding across to another cylinder (unlikely with a single cylinder misfire), if low possibly leak down test to determine where loss is happening but at that point mechanical issue means engine needs to come apart anyway so who cares it'll get seen when apart so a bit of a time and money waster. Maybe pull valve cover to visually inspect for busted valve spring or something.
3. swap ignition coil from 3 to another cylinder, waste spark setup means you only get 2 coils so swap from cyl 1/4 to cyl 2/3 but leave the wires in place.
3.a swap wires/plug boots around if possible (not possible with cyl 1 and 3 sadly) and inspect closely for burn through and arcing.
4. swap spark plugs from 3 to 1 and vice versa, inspect closely for arc over on the ceramic insulator and other visible issues.
5. smoke test intake system to check for vacuum leaks, possible for idle misfire which improves as vacuum decreases when accelerating.
6. check injector signal with noid light for good bright quick flash that gets faster with engine speed and remains bright.
7. swap injectors between cyl 1 and 3, compare resistance values of all injectors to look for borderline values or out of spec values. Inspect sealing o-rings for damage closely.
One more thing to check since you did engine work would be the valve clearances but this isn't part of my normal checks since it's uncommon on a previously normal running engine. If something went wrong and the intake or exhaust valves are not opening enough on that cylinder you can have pretty good compression, no leak down, but poor combustion and misfire due to a low amount of air entering or (or leaving, exhaust won't burn again) vs the amount of fuel being added. That could look like a rich cylinder but not be a fueling or spark issue. It should show up as a bouncing vacuum gauge when cranking the engine with closed throttle or with the engine running but vaccum is funky on a 4 cylinder with a dead cylinder.