I'm pretty sure people have done your mod on here before and ended up with no signal. :(

The base should have a signal booster in it already so adding another isn't going to do much for it.

It will be good to get some feedback as I might just look at the normal version if this is an issue as I like to have the radio.

Found these Carl. :(

http://briskoda.net/forums/topic/88876-changing-octavia-ii-antenna-to-a-shark-fin-antenna/page__p__1088009__hl__shark%20fin%20aerial__fromsearch__1entry1088009

http://briskoda.net/forums/topic/61378-oem-sharkfin-antenna/page__st__20__p__868986__hl__shark%20fin%20aerial__fromsearch__1#entry868986

Remember to take care if you have curtain airbags.

If you can live with the poor reception and don't mind the cost of postage (or bring it to JKM if you're going there) then I'm quite happy to have a go at reworking the board in the old one to see if it can't be got working again.