Hi, how are you all? I am from Argentina living in Mexico, first post, sorry if my english is not so good!
I got a Honda Civic 99 SOHC 1.6 D16Y8 M/T with less than 125000 miles. My story:

I was getting overheating problems, checked up all and it was blown the cylinder head gasket. Repaired that I start the engine fine, drove for 2 nights (cold nights) and noticed when engine warms up it gets pulling. Then another day at afternoon, in very hot weather the engine failed at all, stopped and left me there, called a tow to reach home.

I checked fuel getting to engine and intake, all ok. About ignition I changed sparkplugs, sparkplug cables, and cleaned distributor cap and rotor. Also I changed the ignition control module cause I suspected about it, but it wasnt. The spark was perfectly reaching all sparkplugs.

Then I tried moving distributor out of its bolt holes backwards front of car (advancing timing maybe 3º o 4º, just ½”) and the engine started OK, i checked it with a timing light and it was too much advanced, when i get the distributor back in place, engine continues OK, but when it warms up it stops again alone or when I try to accelerate also stops.

Analysing these tests, I suspected that when I did the gasket repair maybe I reinstalled the timing belt one teeth off so I tried moving camshaft one teeth without belt and reinstalling it. The engine starts good and easily but with a lot of noise, like valves hitting pistons. Now the distributor needed to be at the other side to get good timing. I finally prooved that timing belt was good before cause i checked UP mark on camshaft pulley and timing white mark on crankshaft pulley were aligned vertically and with the moved teeth it wasnt…
I now think it is a distributor problem, but what? Cause I also checked all 3 sensors wiring to ECU and internal resistance of them as service manual, between 350 and 700 ohms.

Also I checked and adjusted valve clearance twice with service manual procedure.

The tests i’ve done were made with jumper on SCS connector to avoid ECU controlling advance and also without jumper.
In conclusión: there is no fuel problems, no ignition coil, ignition module, sparkplug cables, sparkplugs, timing belt position.

I dont think it could be an ECM/PCM problem cause the engine dont start or it is very difficult to, only very cold or if I rótate the distributor out of bolt holes as I said before.

I got a honda interface so i did a scan with my PC, there are no codes or CEL turning on.

Is it possible that distributor shaft gets rotated and it is advancing/retarding spark distribution? Its shaft is one piece with magnetic sold to it to read sensors correctly..

Any suggestions for this problem?
Hope someone helps me! Thanks in advance