If this were my table, I'd do the following:
Side saddle for shotgun; cost and availability of a spare clip, doesn't take up a slot, also doesn't really give you any benefit as the shotgun still needs to be reloaded manually.
I personally wouldn't allow a side saddle for a Crockett EBR since it's magazine loaded. I would allow you to simply tape magazines together or buy two magazines boxed together properly, but again, this wouldn't provide you any benefits except meeting your expectations of what it should look like.
Extended mag in SR4 was 4R, 500¥, and increased the capacity by 25% (rounding up), and I would quite frankly just use the exact same stats. Alternatively, for 1000¥ and at 6R, you could modify the rifle to take Drum magazines. The former would give you a 25 round capacity, while the latter would give you a 50 round capacity.
Since these modifications required a shop and a facility, respectively, to complete, you'd have to hire someone to do the job for you, at a rate of 500¥ per hour, with the thresholds being 4 and 16, again respectively.
As for side mounts, Run & Gun really only specifies one side mount ("one of six places", side being one), but I'd allow a laser sight on one side and a flashlight on the other.