Since this might be of general interest I am going to give a partial answer to this admittedly old question.

1. How many U-boats were based there?

Give or take about 15-20 boats were in the mediterranean at any given moment and there would be others bases (Salamis, Pola etc), so it would be a fraction of this total.

2. How big were the U-boat pens - and what was their location? When, how were they built?

U-boats based at La Spezia shared facilities with the italian fleet, this would be essentially the 19th century navy yard in the west of the city and possibly the civilian shipyards tasked with submarine repairs. There were no bunkers for the u-boats.

3. Did the U-boat base suffer direct air raid damage?

The navy yard was heavily bombed during the war, mostly since 1943.

4. How well defended was La Spezia ie....anti-aircraft guns, flak ships, night
fighters....

To give an idea artillery at the start of the war consisted of:
coastal guns
16 x 76mm
8 x 120mm
26 x 152mm
8 x 305mm

antiaircraft guns
49 x 76mm
24 x 90mm
4 x 100mm
16 x 102mm
Six batteries of 88mm were added in 1943

Fighter cover was provided by the Sarzana air base which had at its disposal in september 1943:
- 17 MC 200
- 3 RE 2000
- 11 CR 42
The CR 42 were usually tasked with night fighter duties at this stage of the war, with a black paint job, masked exhausts and a fixed searchlight.

How much air raid damage did the town itself suffer - and how many people died there -> civilians and services - during the war?

The town was heavily damage, with civilians losess mitigated by partial evacuation measures, shelters etc; still at least a few hundreds of casualties.