Timing marks don't align
 

Hello, everyone.
I'm in a process of replacing head gaskets.
when I was disassembling parts, I couldn't find timing marks (blue or yellow links). The engine was at TDC, marks on cam shaft sprockets (including notches) and crank pulley (harmonic balancer) were aligned. I didn't know and didn't check of intake cam sprocket timing lined up with an arrow on first cam "bridge".
Since I didn't see those blue or yellow links, I marked corresponding links with white out.
Now is the time to install the timing chain... But.. I discovered those colored links, mine are yellow (brass). The reason I didn't see them is that they were "advanced" and were near a fixed guide/rail.
So.. Today I installed the timing chain - intake cam sprockets lined up with "bridge" arrow, yellow links over the timing mark, exhaust cam sprocket aligned to yellow links. But.. the notches on these sprockets did not align... Also a single yellow link at the bottom by crank sprocket didn't align either - it's past timing dot by one link. Also the yellow links of a short chain (at crank) don't align wit timing mark either.
Before disassembly, cam sprocket notches (so called 3 and 9 o'clock positions on exhaust and intake cams resp.) aligned....

See the pictures below.
existing timing marks before disassembly:

https://cimg5.ibsrv.net/gimg/hondafo...32f0a6c7df.jpg
https://cimg6.ibsrv.net/gimg/hondafo...c99047966a.jpg
https://cimg9.ibsrv.net/gimg/hondafo...2338331a82.jpg

Below are the pictures I took now (with timing chain yellow links aligned with timing marks):

https://cimg5.ibsrv.net/gimg/hondafo...c2b35882ec.jpg
https://cimg7.ibsrv.net/gimg/hondafo...70268bba59.jpg
https://cimg8.ibsrv.net/gimg/hondafo...c7cc746a1a.jpg
https://cimg0.ibsrv.net/gimg/hondafo...ed389ee760.jpg

and picture of cam shaft:

https://cimg9.ibsrv.net/gimg/hondafo...35d9c8c452.jpg

All these pictures show loose timing chain - without adjustable rail/guide and tensioner.
I also reinstalled timing chain with old (white-out) marks - same thing - misalignment.

I am puzzled. The valves are all closed and not adjusted yet. I really don't understand why timing belt was:
1 - installed without yellow links aligned
2 - why nothing aligns now...

BTW, the engine was never worked on and no one worked on timing chain or valves. This is a first job that requires some engine disassembly.
obviously, I need you input and advice.

Those links are used for installing only. Once the engine is run those links will only find those positions again maybe 1 in 200 revolutions or more.