Matt
Graham and Annie have given good advice.
I had said to you that I would be pleased to help you but that would have to be when I am in Devon, and on or after mid April I will probably be committed elsewhere.
Having visited you recently and therefore knowing something of the boat and something of you, I would be confident that the junk rig will be no great problem. Indeed you will be able to sort that out on your own. Sort out as much of the rig as you can whilst alongside your mooring.
I would however humbly suggest that your potential problems lie in other areas. Please excuse me if you already know all that I am about to suggest.
You will be taking out a boat which to you is totally new and has just had a major refit. You will have your second hand two stoke outboard on the transom. Although you will have had a chance to test the engine on your mooring, it will be the first time that it has been used in anger. You will initially be unfamiliar with sailing in Plymouth harbour, which has a number of very particular hazards and considerations.
I would suggest that it would be more important to have assistance from someone who is familiar with sailing in Plymouth, rather than someone who knows about junk rig but may be unfamiliar with Plymouth.
You can however do some self help. When you told me of your outline plans I suggested to you that a purchase the 2015 copy of Reeds Nautical Almanac would answer most of your questions. (I did as promised investigate posting my 2014 copy to you but that would have cost more than half as much as buying this years.) I still suggest that you buy this years Reeds. At £36 it is not cheap, but I believe that over the year you will get value from it. (However, I am still a paper publications type; you may be able to get all the information electronically and possibly free.)
By studying Reeds and any other local and free harbour guides you will find that Plymouth Sound up to the Narrows is controlled by the Queen's Harbour Master (QMH). QMH staff operate out of the Long Room which is the obvious control tower on the Devon ie north side of the Narrows. They monitor channels 13, 14 and 16. I think that you will be using a hand held VHF, perhaps without a dual facility, so I suggest that you use channel 13. They are Longroom Port Control or just Longroom. (Double check all this!)
Above the Narrows, Devonport Naval Base and the Hamoaze are controlled by the Flag Officer Devonport. I think that they also operate out of the Longroom but from a separate desk, they use the title Flag and monitor 13 and 16.
The Longroom does have a very good view of much of the harbour but via CCTV they have a view of everywhere in the harbour.
Reeds will also give you the tide times and curve for Plymouth. (Conveniently Plymouth is a Standard Port and the corrections give for times and heights for say Saltash on the River Tamar are negligible for your purposes.)
Now to the rub! You are about to launch an untried boat with an untried engine and an unfamiliar rig into a very busy naval port. The tide swirls and runs through the Narrows at several knots.
You should look at www.qhmplymouth.org.uk . You then need to check on naval activity prior to setting sail into the Hamoaze and then monitor naval activity on the radio. Be aware of the restrictions on approaching the naval dockyard and naval vessels. If you get it wrong the best that you can hope for is an interesting close encounter with a Ministry of Defence (MOD) Police vessel. Even more interesting will be a close encounter with Her Majesty's Royal Marines. At best you will be embarrassed. At worst you will get shot!
If your engine fails and you can't sail because there is no wind or because you have not mastered the rig, you will need to be prepared at all times to anchor. However, anchoring will be difficult in many areas because of the chains of civilian and naval moorings. You may have more luck picking up a vacant mooring, particularly off Torpoint. To assist in that £40 spent on a mooring picking up Gizmo would be money well spent.
Until you are familiar with the harbour and the boat is sorted I would suggest that you avoid the nearby and drying St John's Lake and Millbrook Lake which at high tide will look very inviting.
So, there are a lot of 'Bear Pits'. If you know about them you will be able to avoid them, particularly if you have someone with you who is familiar with the harbour.
Enjoy.
Cheers.
Jonathan