Hi andy,
first of ...welcome

Well i would love to give some clearer recommendations/support, but honestly i hate to say without any more detailed spec's its kind of hard.
Im not too big of an expert on frames and in particular guzzi frame issues.
Maybe though i can help a lil with engine ideas as im working (as a hobby) with pretty good results for the past 10 years on race engines and in particular cylinder heads, with some help of my flowbench that i have been operating for the past 12 years.
Could you give more precise information on the used pistons as i assume the V50 is the usual heron engine?
If possible maybe could you supply some pictures of the pistontops.
Could you let us know the compression ratio?
Do you have any cam spec's of the Joy engineering cam?? Preferably@1mm: EXop/EXcl INop/INcl. Valve lift.
I know the question might sound a lil naive but would you be so kind to lemme know the valve diameters as i would like to avoid digging through stacks of motociclismo d'epoca (i know i have the articles somewhere, buut the search brrrr

) as you might know the numbers by heart
Do you have perhaps have a flowbench (i take it that they where measured when flowed??)diagramm as one can then make more precise assumptions/interpretations.
I dont know to well how sturdy the small block bottom end is, but personally i think that you could still go a lil down on the squish clearance as 1.2mm seems still a lil loose to me for a race bike(on the morinis i went down to 0.8mm's), and heron heads in particular are usually quite grateful for reduced squish.
In the meantime you might like to read a lil into michael mays "firebolt" design which is pretty interesting as he raised surprisingly the compr. ratio as well as the squish turbulence on the Jag as well as on the testbed Passat.
here is one link:
http://www.jagweb.com/jagworld/v12-engine/page4.htmlunfortunately besides that there is not too much info outside of an official SAE paper.
Also you might want to read into michael moores interesting V50 story in case you haven't?
http://www.eurospares.com/v50.htmAs the heron heads are to begin with unfortunately a lil valve restricted one will have to get pretty inventive to collect/find those missing horses regarding jap-bikes(even though with multicylinder japs as tuned CB500's i see it a lil bleak

).
But then CB500's are heavy ricotta-like bikes.
Btw.: if possible and allowed by your race organisation i would advice you to opt instead of the dellortos for Mikuni TM's(the old Sudco TM pro version which is basically a 2stroke carb) as they have a by far superior design of the venturi area, which gives a better signal/response on the needlejet.
With some added effort on the needlejet you should not need a accelerator pump.
For the flywheel i think ed of guzzitech is doing some really nice ligthening job, also i think bruno scola offers a aluminum flywheel from waht it says on his page.
http://www.scolaracing.com/scolaracing_prodotti.htm KIT POTENZIAMENTO PER V35 -50-65-75 Flywhell ERGAL “RACING”
kind regards and a nice weekend
Christian