If you are going to change out the rest of the wood flooring to the gunstock, you will need to do it ASAP. Most "man made" or "factory finished" floors have a shelf life of 18 months. If it has been 9 months already, you may never find enough of the gunstock to complete the rest of the home. For me, obtaining "the rest" of the flooring is of the utmost importance (if you are still thinking that way). The trim can always be painted. And I for one have no problem with the window trim. It is far enough away from the gunstock to "work". The problem comes when the floor and the molding are "touching" (like in your last photos). I would bet the window trim will be fine...but the floor baseboards need to get some paint on them to get rid of this clash. That's about all I would worry about. But first things first - find out if the gunstock is still available. If it is, then you are SUPER luck and should purchase it as soon as physically possible. You are running out of time to "do more" with this engineered product.

To Op- sometimes a cheaply made bypass door will lift off the rollers because of the thin glass the manufacturer used. I have seen doors with 1/8” glass. I never recommended anything less than 3/16, but preferred 1/4” or 3/8. For top of the line, I used 1/2”. Be sure you see and feel theses different thicknesses of glass. Physically, the bypass doors stay in the space because of gravity; they hang on the top track. Therefore, any lifting motion will cause them to come off. One solution is a heavier door. You might look at a 3/8” glass frameless bypass unit. The edges of the glass will be polished, the only metal is attached to your walls so you still have the clean look. In addition, this configuration does use any floor space as a swing/ hinge door does. Again, a good glass company with floor displays will be able to offer you options.

We had a problem with our storm door due to being by the shoes always a breeze and when we opened the door it would take it flying into the column so we ended up removing both doors and installing therma-tru all in one half the door is window /screen couple of levers push up half the window and screen is there We are very happy with it

Holy close ups. You need to back up and take a full picture but for starters there appears to be no door sill. The repair is to pull the unit and install a sill and reinstall or since that looks like a run of the mill steel door buy a new prehung unit and swap them out. Since your picture is so close up it makes it almost impossible to get the full picture of what is going on this is only an educated guess at this point. And from the looks of it the jambs were not procured with the proper jamb depth and they jury rigged extension jambs from plywood instead of pine trim.