Pity JRC don't do a 1kw unit. The Kodens are pretty dissappointing to look at and not real good bang for your buck like the 585 is at the moment. It certainly has the punch. A mate is reading 450m with his 585 with a shoot through hull 600W wetbox transducer. Not going to help you with the descrimination you are going to want Snelly for deep dropping. 1kW is going to be your only option till you can afford 2 or 3kW. Still like the ease of use and menu functions of the JRC over the 585, once again, pity they don't do a 1kw unit. The 585 of the one mate is flush mounted in his dash. It is impossible to look at in any other colour than the white background with red bottom. Pity JRC don't do a 1kw unit! Love the white bottom of the JRC on a black or blue background!
On the 1kW Airmar transom mount transducer, it is easy enough to live with. I may go that way myself in the future. The Seafarer I used at Port Stephens on the shelf had one. Yes I did forget to pull it up at the end of the day and took off on the plane with it down for a bit till I remembered a couple of times. No damage done. It has a breakaway quick release. The 1kW was being fed by a Navnet unit. The tranny plugged into the black box computer. It was dissapointing that backing just in gear in reverse to keep on the bait the turbulance from the prop would still interfere with the tranny even though it is a foot or more below the hull in the down position. I don't know how you bottom fish there. Do you back up slowly or use a parachute/drift anchor?
Maybe Snelly with some fancy marine technition you can change the plugs on your Lowrance 1kW transom skimmer mount transducer. Ymer the 34' Black Watch I am fishing on a bit is using a 1kW wet box Airmar transducer and I wouldn't be surprised if it hasn't been respliced or new plugs put on it at some stage to be fed by a Lowrance X-16C. We were pinging 600m the other week and marked bottom fish (Hapuka/Blue Eye etc.) on a 225m lump 20-30m off the bottom. That is pretty good as Ian (Finding Time) said Black Watch's are renowned for being crappy with wet boxes due to their construction methods.
As for making your own wetbox for a plate boat, it works extremely well. A mate had one on his Try Gullwing. It was reasonable size plate but the clincher was they are extremely deep Ved on the middle part of the hull. All you need is a bit of 6" PVC with a screw cap attached cut to the angle of your hull at the bottom. Screw in one of the bronze trannys to the end cap, fill the siliconed in place bit of PVC with distilled water and Condy's crystals, screw the cap back on and you are away. Another mate did it to the alloy pod on his cat which was possibly greater than 5mm. It did take a bit of sting out of it and the 300W Furuno was only good out to 100m but it does the job. 300W will only get you to 170-180m at the best of times anyway.
As for your Raymarine losing it at 3knots or so, my 600W JRC did much the same with the Airmar transom mounted triducer out on the shelf of Cooktown before Christmas. At 4-5knots or so trolling I could only get to 170m or so no matter what I did, 50 or 200kHz (200 ended up being better). One day to check it out I tried idling in one of the reef openings and pinged 450m. That was the limit. It was only just hitting the bottom on 100% gain on 50Hz. Think it is a turbulance issue. That is why those Furuno transom mounts drop down. That same tranny on ours will read perfectly at 38knots so it is plenty deep enough for day to day use. The shelf will sort any sounder out!