'98 Escort Starting, Idling and running Problem!!!

History - Step son takes car to shop after it stopped on highway and wouldn't start, they tell him timing belt slipped, need to check valves(!) and new belt will cost $2400!!!!
Towed car home, did what they said!! (Stupid) Then found out engine was non-interference!!
Once rebuilt, new timing belt, head gasket, serpentine belt and spark plugs, engine hard to start, idles sometimes and power is down. Removing injector wires on cylinders 2 & 3 has no effect!!!
What's the best way to check injectors and signal to them???

If you put a mechanics stethoscope against the body of the injector while the engine is idling, you should hear it clicking. If you hear clicking on the injectors for the cylinders that dont seem to be doing anything, it could be something physcially clogging up the injector. Anytime the engine is opened up for work there is the risk of crud getting into the fuel rail. I would do a compression check on all 4 cylinders, to make sure you have compression. Then interchange plugs from the other cylnders to make sure it isnt a plug. Mine is a 92, and 98's may be different; are cylinders # 2 and #3 driven by one side of the coil pack? Check to see that you have spark on each cylinder, by pulling a plug wire off and substituting an old spark plug, with the electrode bent up. Working in open air, the spark should be able to jump at least 1/4", if not 3/8".
Although its a lot of trouble, it should be possible to unbolt the fuel rail, and pull the injectors out of the head, leaving them plugged into the fuel rail. I like to wrap the injectors in paper towels and crank the engine (very) briefly. Then I look to see if the paper towels are each fuel-soaked about the same amount. You need to be careful doing this - sprayed fuel ignites incredibly easily. You do own a medium sized fire extinguisher I hope?
On my 92 the spark plugs are fired by an ignitor near the battery rather than by the PCM directly; 2 plugs being fired each time. They seem fairly reliable, but the ignitor is another thing that can quit by 'half'. And in the junkyards they only cost $5 - $15, and arent hard to extract. Make sure the connectors from ignitor to the coil pack are fully seated at each end. (The connector on my Escorts ignitor had a nylon cable-tie to help keep its longish connector from getting loose).