Last July I picked up a '88 311 with 420' and TRS drives. I changed all the fluids and ran her as is. For the winter I ran the pink stuff through her and wrapped her up tight a put a 100 watt light bulb in the engine bay, I'm in northern Michigan. I'll be unwrapping her in a month or so and have a few things I want you do, rebuild the carbs, new dual plane intakes, and distributors. Carbs run great but weep a bit, the intakes look like crap and I'd like to dump the single planes anyway. I had a couple ignition issues over the summer, I'll also be giving her new plugs and wires. Now to the drives, our local offshore boat guy said not to pull the drives unless there is a problem. He says you could do more damage than good. The drives seem solid but I get a little vibration with the wheel at full lock which I expect having experience with CV style shafts in off road race trucks. I have never pulled a drive but I'm not afraid to just don't want to waste time or potentially damage it in the process. Hour meter says 800, and I'd say the boats condition resembles that. The wife really diggs the boat and I want to keep her around for awhile. So, is it worth pulling them? Also the plan is to pull the motors, trans, and drives next winter and rebuild all while she is getting a new paint job.

If you plan on pulling motors/tran's you WILL need to pull the drives off to put the engines back in .....no way around it.
but taking them off will not hurt anything...not sure why someone would tell you not to take them off.
I would take the off just to check the u-joints condition and grease them if they have the zerk fittings. You can also check the motor alignment while the drive is off....hardest part about putting them back on is getting the shaft into the tail-stock of the transmission...

Light bulb probably burned out a long time ago.

When you say you ran pink stuff, hopefully you winterized it correctly. As said, a light bulb will burn out in a few weeks.

Regarding the drives, the u joints need to be checked and greased and bellows and upper seal checked for leaks. How will doing this cause damage?

You will see no difference switching out the Weiand single planes.

I'd save the money on new intakes, unless yours are rotted out, and use it for some fresh valvesprings at bare minimum at 800 hours .

impellors, bellows piece of mind stuff

Impellers for sure!

I would check/replace your exhaust riser gaskets if they show any sign of leaking on the outside, they probably are the inside.
I would check your anti-siphon valves for any debris for your fuel system too.

Not rotted out, just look like crap. The bolt holes for the thermostat is stripped out on one of them. I know I won't see any performance gains but they would look better and can't hurt.