Engine misfires and sometimes even backfires?

Hello, have you tried cycling the ignition switch to retrieve trouble codes? Key on, off, on, off, then on, Check Engine light should flash codes. This is an OBD1 system, they are not as accurate for setting codes as OBD 2 systems.
How much carbon build up was there when you replaced the EGR valve and on the throttle plates?
And has the timing chain ever been replaced, backfires happen when combustion occurs outside of the cylinder. Overly rich mixture stretched timing chain causing valve timing to be off. a rich mixture and/or weak spark, carbon build up will cause backfires.
How long ago were the spark plugs replaced? You can use a test light hooked to ground to check how far the spark can jump, just don't hold on to the spark plug wire, have the spark jump to the test light. Unless you have a spark tester that has an adjustable gap.

Here is a guide to help:

https://www.2carpros.com/articles/engine-backfires-while-running