Trying to figure why she wont start once warm?

Well after much waiting and sourcing of parts from ebay etc I have redone my charging electrics.

Purchased a Ducati 996 stator off ebay for AU$90 which has bigger gauge wiring from the coils to the connector for the yellow wires,
bought a 04-06 R1 R/R(Shindengen FH011AA) from ebay us for AU$80 delivered
bought a new YTX14-BS battery locally for AU$105 and then set about rewiring all the above with better connectors and more wire.

I replaced the 3 pin connector at the join between R/R to stator wires with a waterproof unit,
ran heavier gauge wire from R/R+ terminal directly to the battery+(with a waterproof 30amp fuse in line) and coupled the original wire from the starter relay into this wire.
I ran the wire from R/R- terminal directly to the battery- as well as another wire coupled to this straight to the frame ground.
Had to drill two new mounting holes and used heat sink paste all over the back of the R/R before fitting with longer bolts and nuts to hold in place.

Once everything was connected I fired her up and she sounded great
tested on cold start up with choke on fully and lights on and readings as follows:
idle 13.56vdc
2000rpm 14.38vdc
4000rpm 14.22vdc
then once I had the gear on it was time for a ride to see whether the restart issue was gone and to test voltage once home.
Rode for 30+mins and got her nice and hot(operating temp that is ) then back home to check readings which are as follows:
idle13.46vdc
2000rpm 14.24vdc
4000rpm 14.32vdc
and 5000rpm 14.32vdc
much better voltage readings and the new R/R was cool enough after the ride that I could grab it and hold it with no real heat obvious

so it looks like I have finally fixed my restart issue as every time (6) I restarted her she fired straight up and fired easier than she has since I bought her back in Sept 09.

If anyone is interested in upgrading the R/R I would recommend the FH012AA as I had to cut 1cm off the fins on the FH011AA to get it to fit behind the seat cowling.