Hopefully I am understanding your question correctly here....
The main benefit of the custom 404 page aside from the obvious improvement to user experience is that you provide additional links into content that otherwise wouldn't necessarily be available to the search bots.
In essence if you just had a standard 404 error page you'd send the search bots to a dead page where their only decision would be to leave the domain and go elsewhere.
Regards setting up 301 redirects I like to associate a cost to each 301 redirect. Imagine the time it will take you or someone else to set each redirect up (say $5 per redirect). Then consider the following:
Is the URL that is 404 worth redirecting?
(1) Does it hold some residual SEO value (i.e., is it present on external sites that is driving link equity? if so can you redirect that equity to somewhere more valuable?
(2) Is the URL present on an external site driving referral traffic? if so do you have a new content page that will still match the users intent?
if the URL(s) that are 404'ing have no real link equity associated to them and/or you don't have a genuinely useful page to redirect the user to then I would just let them hit the 404 page.
If in doubt put yourself in a users boots and ask yourself if the set-up you have done would offer a valuable experience? no point redirecting a user to something totally irrelevant to the original intent - it'll just p!ss them off most the time and increase your bounce rate.