Mr Carlos Fernandes, Curator, Goa Central Library, Panjim, says that Prof. Suresh Amonkar of Mapusa has recently donated a MS of the KP to the GCL. It would appear that the MS had been gifted to him by Bishop Allwyn Barretto of Sindhudurg. Perhaps the MS had been lying around in some church in that diocese. (Mr Amonkar is currently translating the KP into Konkani. I believe excerpts have been appearing in some magazine in Goa.)
The Arambol MS which had been mentioned to me by Fr Agnelo Pinheiro of Rachol Seminary turns out to be a copy of J.L. Saldanha's The Christian Puranna. It is currently in the possession of the Rachol Seminary.
I went yesterday to the Goa University Library. Vast enough building, not very well kept. Lots of 'collections' - which I believe are book holdings donated to the library by distinguished individuals. A copy of the KP is in the Vagh Collection, which itself seems to be part of the Pissurlenkar Collection. The librarian in charge was busy, so I did not get a chance to have a look at the MS.
I still have to visit the Thomas Stephens Konknni Kendr / Xavier Centre of Historical Research, Panjim, to see their MS of the KP.