Sounds like you are on the right track on diagnosing this issue. You are correct, the 1998-1999 Corollas were MAP based, and do not have a MAF sensor. Definitely sounds like a fuel or fire issue (fuel system and induction or ignition related).
A clogged fuel filter is a possibility, but they generally get worse as the demand for fuel increases (increase in engine RPM, increase in fuel). But since the car is a returnless fuel system type (almost every car out there is this way now) - that instantanous need to more fuel, the fuel pressure regulator could be overwhelmed as the system meters out fuel as indicated by the ECM. Both the filter and the regulator are on the fuel pump assembly, which is inside the gas tank. Have to pull the rear seats out to expose the access panel, and pull the whole assembly out.
Loose plug wires and/or fouled plugs (plug gap is not consistent, wires making intermittent contact), or overheated coil packs may also be a source of the problems. The engine could be intermittently missing, but not really noticeable unless you push the engine a litter harder, like accelerating briskly.
A leaky vacuum hose or other vacuum leak, dirty throttle body, loose throttle cable, bad connection to TPS sensor on throttle body, clogged injectors are other possibilities as well.
Start off with the easy stuff first - double check the plugs (pull them out and read the ends), verify the gaps are consistent and you are running all the same plugs, recommended specs (I've had different plugs mixed up in the box before - anything can happen). Make sure the plug wires are securely attached. Run a bottle of fuel injector cleaner / run a tank of premium fuel to rule out a missing engine due to heavy carbon deposits in the engine.(if the car runs better - then you need to have the carbon blown off, either run it hard on the highway or try a number of decarbonizing methods - just be careful). Fuel pressure test will definitely tell you if you hae a fuel delivery issue - unfortunately, it is non-trival to measure puel pressure on the car. You'll have to get a fuel line "T" connector fitted to the fuel hardline under the hood and monitor the fuel pressure in realtime. Cleaning the throttle body is pretty easy to do - you can also double check for leaky vacuum lines and if there is too much slack in the cable while you clean it.
Is this something that has just gotten worse over time or something that just suddenly started.
