I suggest to try DRVTEST for testing all signals.

Anyway, on real machines the FORMAT say not ready when problem with Index pulses. Drive with faulty Index signal can Sector Read/Write, but fail at FORMAT.

When executing Step/Seek/Restore commands, motor also will turn on, and drive become ready?
Format firstly do SD/DD check. Do 50 STEPIN then counting how many STEPOUT needed for a Track 00. Also report Not Ready if still no Track 00 after 256 STEPOUT.

cannot see changes on DRVTEST on pin 2 and 34 (always blue)

The firstly test Read Address command in DRVTEST.
Needed display data, and got a OK.
If head at wrong position the different data marked as red.
(Attachment Link) (Attachment Link)

Then test Read/Write Track. Put EPDOS 1.x ROM to your configuration, start it and enter to DISK EDITOR.
Switch to TRACK EDITOR mode.
Track readed, usually got a Data error, because now all data handled as raw data, including CRC bytes. Don't care about it
(Attachment Link)

Then make a new FORMAT template to buffer, for example with FORMA9. Then press WRITE. It is needed to be completed without error.
(Attachment Link)

Ok, now we know why not works the FORMAT

Then look about your track command emulations. Are these implemented at all?
In ep128emu Read Track not implemented, but this is not too important.
At Write Track, it is gather the sector addresses and sector data fields from the raw track byte stream and write the data for the right sector in the disk image.
Then formating will work, just you can't use different format than the existing format of disk image format. For example you can format 720K disk to 720K, but can't to 800K.

0 are wrong value, because the sectors numbered from 1...

The current value are "random", it is return with a firstly found sector header, soo depending the current disk position while rotating. But with 720K disks need it from 1 to 9.
On a non rotating disk images practicaly will be 1 the first, if more addresses readed, then 1,2,3... until max sector, then start again from 1.

Anyway the Track and Head fields are the most important data. Head used for a check for single sided drive at Format. And also when read disk information: if it is two sided disk, check for one head drive, and report Incompatible disk if this is the situation.
Also at disk check do some Step In, and read address and verify Track number. If it is right, then nothing to do.
If it is 1/2 value, then 40 track disk in 80 track drive needed to use double stepping.
And if 2x value the 80 track disk in 40 track drive, report Incompatible disk error.