Many important points have been raised in the present topic.
As pointed out by a member - Koba is exceptionally user friendly repository. It served me PDF within a record time of 1 day. They have some MSS scanned. If a scholar places a request they scan the MSS out of turn. Contact details are
gyanmandir@kobatirth.org and kobatirth@gmail.com. They have MSS from their centre as well as scanned photocopies of MSS from Patan, Jesalmer and BORI among other MSSs. So if you fail in securing from Patan, Jesalmer or BORI, this source should help you out. They also have a large collection of digitized Indology related books and journal articles with well maintained database. For searching especially jainist sources, this place is wonderful.
As regards the other private repositories, my experience has been very lukewarm.
As regards the digitization program, one good cataloguing exercise by GOI is online at http://namami.org/.
Their report says that they will be launching an online digital manuscript library, but it has not yet materialized.
In the meantime I have prefferred an appeal under Right to Information act, 2005 to the National Manuscript Mission seeking all digitized MSS. Their response in appeal is a bit encouraging. Find the response attached to the mail. Couldn't scan, so just took photo from mobile. If the appeal succeeds, we may get all the MSS digitized by National Manuscript Mission in free domain. (Will need to arrange for funding then :) )
I also sincerely urge the members to use Right to Information act to the fullest. (http://rti.gov.in/rti-act.pdf). This makes it mandatory for any Government Institution to provide copies of records to the information seeker, with punitive action for failure. Of course, this right is given to only Indian citizens, but I guess we can arrange a local Indian scholar of our acquaintance to do the application on our behalf. The fees are also very nominal. Application fees INR 10 - 50 depending on the state. Copying fees - 2 rs/ page mostly. DVD charges - 50 rs / DVD.
Appeals are without fee. So you can continue your battle as long as you win. Currently my appeal is pending in court of Information Commission against the order of National Manuscript Mission. So, if your efforts have not succeeded in securing a manuscript from a Govt repository, you may like to give this legal right a try.