Best way to fix bad ties in simultaneous chords on two staves?

[Ophir Lifshitz]

Hi all,

Here you can find my code and the output rendering here:

https://gist.github.com/hftf/b7d83b58e9429dddacb0

What is the best way to fix the short ties in the lower staff and dubious tie placement in the upper staff, while keeping both staves aligned?

Thanks in advance.