For me this is serious. So please do not recommend just any teacher, who knows a lot about fighting. 
Alaikum salaam Mikael,
Similar to a previous posts, it pays to define what do you mean by the 'spiritual side of silat'. Spiritual, supranatural, tenaga dalam, kerohanian, kebatinan etc. may mean different things to different people.
For some it may mean the ability to do almost supernatural things relative our 'normal' perception such as the invicibility from bullet or knifes, no contact punch, seeing with your eyes closed etc. To other it is simply how to become a better person (not much different than phylosophy of Karate, kungfu or boxing for that matter) or to submit and surender completely to God's will (After all this is what Islam is all about, right ?).
Another thing that you will need to define is, as you also mention the word, the what do you call 'shirk' or syirik or your 'treshold level' of it for wanting of a better word.
Would you consider a ritual of fasting (either fully or only consuming rice and water, 'mutih') for 40 days topped with seclusion without any light (pati geni) as syirik or bid'ah?
What about bathing using or drinking water from 7 different wells laced with flower from 7 different gardens treated with invocations (mantra) from the master?
Or dzikir and du'a send to and sometimes asking intercession (washilah) from the late grandmasters, syekh Abdul Kadir Jaelani or Syaidina Ali bin Abi Tholib recited in Arabic, Javanese/SUndanese or combination of both. In many cases it need to be done in 'sacred places' such as in a grave of some saints.
Or receiving a talisman (jimat) from the master, be it a keris, ring with special stones, metal implanted under your skin (susuk) or soil from 3 different graves wrapped in papers with some Quranic verses written on it with the mention that as long as you wear them you will be safe from any harm ?
Or what about good old fashioned breathing based meditation spattered with terms of chi or prana which is not associated with Islamic tradition not to mention some concepts that will made a syariah-based purist shudder such as the unity of God and the Creations (Wihdatul wujud, manunggaling kawulo gusti).
Apology for long lists of examples, but they are certainly some of the methods used in many 'spiritual study' in silat, so you need to consider them before hand.
Back to the your question, there could be several option. One is to consider a tharekat based 'path' such as Qadiriyyah, Naqsabandiyah or Sanusiyah. While they are not directly related to martial arts in the physical sense, many of the old silat master had been known follow it at some stage of their live. The more well known example of it is the Pondok Pesantren Suryalaya in Tasikmalaya west Java (
www.suryalaya.org) . I had several pesilat friends, both Indonesian and caucasian that spent some times there for their spiritual retreat and came back very satisfied. I believe there are others like it somewhere else.
Secondly you can try to contact some silat school which is commonly associated with well known Islamic organisation such as Pagar Nusa ( with Nahdhatul Ulama), Tapak Suci (Muhammadiyah), Thifan pokhan (Partai Keadilan Sejahtera), ASAD (LDII) etc. Google search on each names will give you some idea of what they are.
Thirdly, well find a private teacher that are willing to teach you. May be other sahabat silat in this forum can point you out to the right direction.
Salam, cheers
O'
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