Remind me again. When the crank is fully straight, should my leg be fully straight? Cos at the moment it pretty much is and I'm thinking that in combination with my large cranks cos be causing the discomfort in my knees?
Regardless of the fact that you're using different muscles in the recumbent position, it's pretty the same as DF position when it comes to leg length on a fully extended crank. It sounds like you want to adjust the boom slightly so your knee is bent a little more on this fully extended position.
But you may also be getting problems with these large cranks as you describe them on the up stoke too. If they're too long then this might be causing a little strain on the knee when you begin the down stroke [when the knee is closest to your chest].
Leading on from that, what seems to be favoured a lot by recumbent riders are shorter cranks, the exact size depending on the length if your leg. It's not uncommon for riders to have 150mm. Changing the crank length will also affect the gearing. In effect you'll be adding at the high end and losing on the low gears due to a change in leverage.
A lot of recumbent riders swear by them, particularly in relation to knee problems. Personally I'm happy with 170mm, but being 6ft 3in that is probably about right for somebody my size anyway.
It's another one of those personal, try it and see, experiments. See if you can try some somewhere before you buy. They can be tricky to source.
There's loads of stuff out on short cranks out there on the web.
Brol is a good place to start.