Anything a Seeker can do another class can do better. Much better.
Here are the trends, there are exceptions, but they are rare. I will compare Seekers to real controllers, like Wizards, Invokers and Psions, WIP for brevity. Hunters are comparable to Seekers.
Survivability
Seekers have more HP and lower AC than WIPs (Wizards and Psions have to take a feat to achieve this). Seekers have one of the best Will in the game, and this is the most important non-AC defense.
These mostly cancel each other out, and does not even matter if the defender does his job right.
If the enemy gets to you however, WIPs mostly have Staff Expertise, but a Seeker has to invest in getting away. A minor Shift is nice, but does not help in difficult terrain or in a grab.
Control
Seekers create lots of difficult terrain. This is good in low heroic, but after that you meet many creatures with Reach, Flight, Teleport, Forced Movement, or simply Shift 4. For them difficult terrain does not really matter.
Level of control
Seekers mostly do soft control, like "the target takes Dex damage if it moves". First, the damage is too low to matter after low heroic. Second, even at low levels the choice is the DM's, so if you have one with a good tactical instinct, you do not achieve anything above a Ranged Basic Attack.
Compare this to the hard control of the WIP: "the target can not shift/move, or is prone, blind or dazed."
Number of targets
WIPs annoy lots of targets, or shut down one entirely. Seekers mildly annoy one.
Defenses targeted
Seekers attack AC, that is mostly the highest defense. In paragon you can get the Deft Blade feat, to make Basic Attacks target Reflex, but the Light Blade limitation hurts your damage. WIPs have access to lots of nice attack powers vs Will out of the box.
Of course Seekers have the proficiency bonus of their weapon to compensate, so this is supposed to be equal. In practice however, WIPs have the flexibility of attacking the Will of a Brute, or the Fort of a Skirmisher.
Conclusion
If you are so inclined, you can build a comparable single-target Controller from a Figher, Warlord, or Warlock, while staying much better at defending, leading or striking.
Damage
The only redeeming factor of the Seeker. With a Hungry Gouge you can do respectable damage.
If you go for precision, Superior Crossbow is also great, and you do not need those minors anyway.
In paragon you can get the great Primal Eye feat, to add your secondary attribute to RBAs. But this is accessible to anyone with a multiclass feat, I have seen a Sorcerer with it.
Feat Support
Aside from Primal Eye, Seekers have no feat support worth mentioning. Invokers and Psions have great class specific feats, not to mention Wizards.
Overall
A Genasi Wizard with the Elemental Empowerment feat and a Lightning Staff will do comparable damage and better control, against twice or three times as many targets as a Seeker.
With the Seeker a heavy optimizer can achieve the level of usefulness of a vanilla Wizard. Sometimes it is a good thing, in a non-optimizing party this can be used to avoid the tension between the optimizer and others.
Because of the math of DnD4e (one monster for one player), you are only an asset to your party if you are stronger than the average monster. For this reason do not give a Seeker to a beginner.
They should stack.
Assuming you are using version 3 of the Mystic Class the +3 ability is Psionic Weapon:Augmented Weapon, and the +4 is Hone the Blade class feature of Order of the Soul Knife, I see nothing immediately that would preclude you from stacking these bonuses. It would cost you 12 points, and the former is a 7 pt ability, meaning you would not be able to use it until 9th level.
Your DM may be thinking of the rule about figuring things like Armor Class, where you can only have one formula, and you can choose the more favorable one. In general, in 5th Edition, Formulas may be used once, but bonuses do indeed, stack.
Best Answer
There are no options in any of the core D&D 5e books which allow "retraining" a class using any definition of "retraining" that I can think of.
The only options for training of any sort I see at all are:
The PHB offers rules for multiclassing (p163) but this isn't so much "retraining" as it is training in a different field entirely.
The PHB (p187) presents training in a tool or language as a possible downtime activity. It says, "Your DM might allow additional training options." It takes about as long as a public school year in the US to complete one training option.
The DMG (p131) presents optional rules for training to gain levels. That is to say, with these optional rules you must spend gold when you reach the required XP value to gain a level. This training lasts about 2 days per level.
The DMG (p231) also presents rules for granting training as an "alternative reward." That means this option is presented as an alternative to magic items, so you're not going to be able to just go out and do it. You can spend the same amount of downtime that the PHB requires for training to learn a new skill, gain a feat, or gain inspiration daily for about a week. You'd have to ask someone else how 7-10 days of inspiration compares to a permanent skill or feat, let alone would be worth the 9 months of investment to get it.
However, keep in mind this is 5e, not 3e, and the game takes great pains to remind readers that the DM can use whatever options they want in their game, including those they devise themself or adopt from other games.