The plan and sketchup perspective are helpful. It was the deck along the side that I wanted to know about. If you limit the width of the swale to only about 4', you may not be able to achieve enough capacity to hold all the water during a torrential storm. I'd widen the swale to about half the distance between house and fence. Making it wider is fine, but the wider it is, the larger the retaining wall must be. Though I said I'd avoid creating the swale below the deck, I will now eat my words. Often, in a remodel situation--especially with limited space and where everything around is already built up--one cannot do everything in the perfectly ideal manner. But in creating it under the deck, I'd make sure it's wide enough to have sufficient capacity. In the sketch, I'm showing the deck using the wall as a support, but whether you could do that, or not, depends on how things shake out in the relationship of finish floor elevation (ffe) to existing grade. You seem like the kind of guy who would have a nice laser level, or need an excuse to buy one. You might some evening use one to mark the ffe directly on the grade (with paint) so you can get a nice visual of what you're dealing with. Depending, you may be able to create a secondary swale at the top of the wall and disperse the water before it goes into the primary swale. But because of grade and roots, that might not work out. You also might build the wall higher than I show and connect the deck to its side. Or, the deck may be independent of the the wall. Hopefully, you can understand the sketch of the drainage scheme. The arrows indicate that you must drain water away from your house at ALL sides. Near the back, it collects in the swale and is moved around the house to lower elevations on its way toward the front. I would not be much concerned about the tree roots. The prior disturbances are long ago and trees have nothing better to do than grow replacement roots, so they've long ago been re-established. The rear-most tree will maintain more than 3/4 of it's roots in spite of your building a wall in its vicinity. Near the front-most tree, if you end the wall aiming directly at the trunk, as I've shown, you will have little need to remove many large roots. It can recover from other excavation you do in the vicinity. (See the part of the sketch, in red and black, floating above the deck.)

In Australia and many places in Europe this second floor drain is a most and required by their countries "Plumbing Code". I think these second drains should always be used with a channel drain / curbless shower installation. I reviewed this subject with my local plumbing inspector and he informed me that a plumbing system designed and built properly to code does not need the second drain to pass inspection. "But is it a good idea?" I think so. David's concealed drain the most applying concept to me so far! - buried under the vanities kick or deep behind a free standing or floating piece (a second channel drain up tight to the baseboard?). Some of the options for designer drains available through California Faucets are amazing - all the top bathroom shops carry them. This second drain and fail safe would offer up better protection if a clog caused by blocked hair, wash cloth, foot, toys ("Little People & their stuff") went unnoticed in the Peak of Play Time. There are issues with priming this second drain line and many was of doing just that - have a ticketed plumber help you with the lay out to be approved by city hall. My kids bathroom floor is heated and I slopped this floor a hair so dripping water would not sit up against the tub base and baseboards (Wood). If a drip or slow leak happen I hope this will bring it out to the center of the room for us to notice and repair. I designed my daughters vanity piece to have 6 drawers, 2 sinks and an open back to work on and service the plumbing connections. In my en-suite I will rip up the floor and follow David's advice on a concealed back up drain. This second drain will cause my curbless shower to have compound angles so I'm thinking we should look at a 4"x4" tile or smaller for the floor. More work.... Safer.... Nice.... Perfect.

In general, landscape design looks at the clients' needs and wishes for the property as a whole and the creates a design that then meets as many of those as possible in the most pleasing way. Other than the sheds and the veggie garden, how do you want to use the yard? To my mind, that needs to be answered before any real plans are made. Is privacy (fence) more important than the veggies? Does it need to be there year round, or is privacy only really important in the summer when you will be outside more? Do you want a large open space for games or running around in the center? How much shade is there over the course of the day along the chain link or in other spots of the yard such as along the deck? Do you want a "pretty" yard or a kid-friendly yard or is the growing of food more of a priority or are they all of equal priority? Where will you be most likely to walk or drive and so will need to be left open? Where is water available, and would you be able to add hose bibs in other spots as needed? Do you want afternoon shade for the deck or other areas, and would you be more likely to plant a tree, or add a structure such as an arbor or shade sail? What other wishes do you have for the yard? As others have said, the more sun, the more successful the veggie and fruit beds will be, so too close to the sheds and the nearby solid fence which will provide shade should be avoided. You also will want to change your grouping/way of thinking about the plants from culinary to cultivation. Melons, like all your veggies, are annual plants, while most other "fruits" you have listed are perennials. The annuals and perennials each should have a planting area so that when clearing out and replanting annuals each year you aren't disturbing the perennial plants. The strawberries will need renewing every few years while each of the the shrubs and vines, which are fairly permanent, have different maintenance needs, and so should be planted in separate areas. If you grow herbs, some are annuals and some perennials. Consider overall goals and how else you will use your yard to help determine the best spot for the veggie beds. For instance, if you want the center of the yard left open, then think about putting your food plants along the chain link instead of a fence since it looks like it gets good sun. Or is the solid fence important enough the you should stockpile your soil for now or make temporary beds and then when the fence has been added, create the beds and plant food crops? Could you use the berry bushes and kiwi vines for your privacy instead of a solid fence? They are deciduous, so wouldn't be great for winter privacy. You would need to leave room between the shrubs and the chain link for accessing the vines. Fruit plants don't need as close access as herbs or veggies since fruit tends to be picked in chunks, while veggies tend to get harvested for particular meals, so think about putting the veggies and herbs closer to the house where there is easy access from the kitchen. Would you want veggies as a border around the deck, or does that either not fit the plants' needs or your wishes? So create a list of uses and priorities for the yard as a whole (swimming pool? play structure? bocce court? badminton net? trash can storage? etc, etc), prioritize them, and then start thinking about placement. You have already made one big decision, the shed size and placement, and so before making others, I would stop, step back and look at the yard overall. Take some time over the next growing season to look at sun and shade patterns (if you map sun as it changes from the vernal equinox until the summer solstice, you will have a good grasp on how it will look but in reverse for the rest of the growing season) as well as wind before planting anything permanent if successful cultivation of food crops is a priority. Once you have a good handle on growing conditions and your overall goals for the yard, then you will have a better idea of where is the ideal placement for each of the various uses you have for your yard.

Once your building footing/foundation is waterproofed, this: Remove dirt as needed to slope the dirt in that path away from the building for about the same measurement as the overhang of the building and end that slope with a level space at least a couple of feet wide. . On the far side of the level space (at the embankment), that is where I'd dig my shallow ditch for the footing and foundation for my concrete block wall. In the level place I'd dig down about six inches -- deep enough to add a few inches of packed sand atop which I'd arrange cap blocks as stepping stones, between which blocks' I'd add gravel to help enable the water run off. https://www.paving.org/index.php/how-to-lay-stepping-stones-on-gravel/.  What I'd do on the short slope by the building beneath the overhang would depend upon what, if anything, might grow there. Since it is likely shady, my inclination would be remove enough dirt to create a sloped wall with large heavy rocks or pavers or cap blocks below the siding. https://www.houzz.com/discussions/6034526/retaining-wall-on-slope#n=3 You could do the same on the other wider sloped side beside your gravel/paver/block walkway but, because it is steeper, you may need to hold the bottom row of the rocks or cap blocks in place with concrete/cement -- then you may be able to space the others with moss or ground cover planted in between them or fill the area in between with more gravel.